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Better statistics with higher gap penalties


A second search of SwissPROT using CAR1_DICDI is shown below. The SSEARCH (Smith-Waterman) program was used with the BLOSUM50 matrix and gap penalties of -14 for the first residue in a gap and -2 for each additional residue. Now, the highest scoring non-G-protein-coupled receptor sequence has an expectation value of E()=0.4. As before, rhodopsin R and calcitonin/secretin C/S members are noted.

The best scores are:                               s-w Z-score E(43470)
CAR1_DICDI CYCLIC AMP RECEPTOR 1.                  2678 3668.2  0
CAR3_DICDI CYCLIC AMP RECEPTOR 3.                  1520 2074.2  0
CAR2_DICDI CYCLIC AMP RECEPTOR 2.                  1493 2039.4  0
CALR_HUMAN CALCITONIN RECEPTOR PRECURSOR (CT-R).    155 197.6 0.00015  C/S
CLRA_RAT CALCITONIN RECEPTOR A PRECURSOR (CT-R-A)   150 190.9 0.00035  C/S
CLRB_RAT CALCITONIN RECEPTOR B PRECURSOR (CT-R-B)   150 190.2 0.00038  C/S
YOW3_CAEEL PROBABLE G PROTEIN-COUPLED RECEPTOR ZK6  141 177.8 0.0019
DIHR_MANSE DIURETIC HORMONE RECEPTOR (DH-R).        132 167.8 0.0067
IL8B_HUMAN HIGH AFFINITY INTERLEUKIN-8 RECEPTOR B   128 163.2 0.012  R
GLR_RAT GLUCAGON RECEPTOR PRECURSOR (GL-R).         128 160.5 0.017  C/S
VIPR_HUMAN VASOACTIVE INTESTINAL POLYPEPTIDE RECEP  123 154.2 0.038  C/S
CALR_PIG CALCITONIN RECEPTOR PRECURSOR (CT-R).      123 153.7 0.040  C/S
G10D_RAT PROBABLE G PROTEIN-COUPLED RECEPTOR G10D   118 148.6 0.079  R
IL8B_RABIT HIGH AFFINITY INTERLEUKIN-8 RECEPTOR B   115 145.3 0.12   R
RDC1_HUMAN G PROTEIN-COUPLED RECEPTOR RDC1 HOMOLOG  114 143.8 0.14   R
SCRC_RAT SECRETIN RECEPTOR PRECURSOR.               115 143.3 0.15   C/S
GLPR_RAT GLUCAGON-LIKE PEPTIDE 1 RECEPTOR PRECURSO  115 143.1 0.16   C/S
IL8A_HUMAN HIGH AFFINITY INTERLEUKIN-8 RECEPTOR A   111 140.0 0.24   R
GRFR_RAT GROWTH HORMONE-RELEASING HORMONE RECEPTOR  112 138.9 0.27   C/S
OPSD_SPHSP OPSIN.                                   109 136.6 0.36   R
VIPR_RAT VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTO  110 136.3 0.38   C/S
>>VME1_CVPFS E1 GLYCOPROTEIN PRECURSOR              106 135.6 0.41 <<
GRFR_PIG GROWTH HORMONE-RELEASING HORMONE RECEPTOR  109 135.0 0.45   C/S
SSR1_RAT SOMATOSTATIN RECEPTOR TYPE 1 (SS1R) (SRIF  108 134.9 0.45   R
TA2R_MOUSE THROMBOXANE A2 RECEPTOR (TXA2-R).        105 132.0 0.66   R
>>ARP_PLAFA ASPARAGINE-RICH PROTEIN (AG319) (ARP)   107 130.8 0.77<<
OPSD_HUMAN RHODOPSIN.                               103 129.0 0.96   R
GRFR_MOUSE GROWTH HORMONE-RELEASING HORMONE RECEPT  104 128.7 1.00   C/S
TA2R_RAT THROMBOXANE A2 RECEPTOR (TXA2-R).          102 127.8 1.12   R
IL8B_RAT HIGH AFFINITY INTERLEUKIN-8 RECEPTOR B (I  102 127.5 1.18   R
??SUP2_PICPI OMNIPOTENT SUPPRESSOR PROTEIN 2.       106 126.6 1.32 ??
AG2S_XENLA TYPE-1-LIKE ANGIOTENSIN II RECEPTOR 2 (  101 125.9 1.44   R
>>CYB_CROLA CYTOCHROME B (EC 1.10.2.2).             101 125.5 1.51<<
>>GABP_ECOLI GABA PERMEASE (4-AMINO BUTYRATE TRANS  102 125.1 1.59<<
OPSD_RANPI RHODOPSIN.                               100 124.8 1.67   R
CRFR_RAT CORTICOTROPIN RELEASING FACTOR RECEPTOR P  101 124.8 1.67   R
PRA1_USTMA PHEROMONE RECEPTOR 1.                    100 124.7 1.68
GRFR_HUMAN GROWTH HORMONE-RELEASING HORMONE RECEPT  101 124.6 1.70   C/S
>>PACR_RAT PITUITARY ADENYLATE CYCLASE ACTIVATING   102 124.1 1.81<<
>>CYB_CYPCA CYTOCHROME B (EC 1.10.2.2).             100 124.1 1.81<<
OPSD_CHICK RHODOPSIN.                                99 123.5 1.97   R

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