BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 039996
(241 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QD1|A Chain A, The Crystal Structure Of The Formiminotransferase Domain
Of Formiminotransferase-Cyclodeaminase.
pdb|1QD1|B Chain B, The Crystal Structure Of The Formiminotransferase Domain
Of Formiminotransferase-Cyclodeaminase
Length = 325
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/115 (22%), Positives = 50/115 (43%), Gaps = 8/115 (6%)
Query: 6 LTCCKVYISESQNKAALESIEQAARLFSAAIIVNKFEDVTYNRVGYTVVSKLAPTLSSDS 65
L C SE +N+ +++I +A ++++ + NR YT V + +
Sbjct: 3 LVECVPNFSEGKNQEVIDAISRAVAQTPGCVLLDVDSGPSTNRTVYTFVGRPEDVVEG-- 60
Query: 66 CPLKSTVFAMIKAAFENIEPGMHSGSHPRLGVVDHICFHPLASAPLDQVAGIAKS 120
+AA++ I+ H G HPR+G +D F P+ +D+ A++
Sbjct: 61 ------ALNAARAAYQLIDMSRHHGEHPRMGALDVCPFIPVRGVTMDECVRCAQA 109
>pdb|1TT9|A Chain A, Structure Of The Bifunctional And Golgi Associated
Formiminotransferase Cyclodeaminase Octamer
pdb|1TT9|B Chain B, Structure Of The Bifunctional And Golgi Associated
Formiminotransferase Cyclodeaminase Octamer
pdb|1TT9|C Chain C, Structure Of The Bifunctional And Golgi Associated
Formiminotransferase Cyclodeaminase Octamer
pdb|1TT9|D Chain D, Structure Of The Bifunctional And Golgi Associated
Formiminotransferase Cyclodeaminase Octamer
Length = 541
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 33/145 (22%), Positives = 56/145 (38%), Gaps = 23/145 (15%)
Query: 5 MLTCCKVYISESQNKAALESIEQAARLFSAAIIVNKFEDVTYNRVGYTVVSKLAPTLSSD 64
L C SE N+ +++I QA ++++ + NR YT V +
Sbjct: 3 QLVECVPNFSEGNNQEVIDAISQAISQTPGCVLLDVDAGPSTNRTVYTFVGQ-------P 55
Query: 65 SCPLKSTVFAMIKAAFENIEPGMHSGSHPRLGVVDHICFHPLASAPLDQVAGIAKSVVGD 124
C ++ + A + A + I+ H G HPR G +D F P+ D+ AK+
Sbjct: 56 ECVVEGALSAA-RTASQLIDXRKHKGEHPRXGALDVCPFIPVRGVSXDECVLCAKAF--- 111
Query: 125 IGSGLQGVIVIGSTRWVDNYNIPVF 149
R + N+PV+
Sbjct: 112 ------------GQRLAEELNVPVY 124
>pdb|2PFD|A Chain A, Anisotropically Refined Structure Of Ftcd
pdb|2PFD|B Chain B, Anisotropically Refined Structure Of Ftcd
pdb|2PFD|C Chain C, Anisotropically Refined Structure Of Ftcd
pdb|2PFD|D Chain D, Anisotropically Refined Structure Of Ftcd
Length = 541
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 33/145 (22%), Positives = 56/145 (38%), Gaps = 23/145 (15%)
Query: 5 MLTCCKVYISESQNKAALESIEQAARLFSAAIIVNKFEDVTYNRVGYTVVSKLAPTLSSD 64
L C SE N+ +++I QA ++++ + NR YT V +
Sbjct: 3 QLVECVPNFSEGNNQEVIDAISQAISQTPGCVLLDVDAGPSTNRTVYTFVGQ-------P 55
Query: 65 SCPLKSTVFAMIKAAFENIEPGMHSGSHPRLGVVDHICFHPLASAPLDQVAGIAKSVVGD 124
C ++ + A + A + I+ H G HPR G +D F P+ D+ AK+
Sbjct: 56 ECVVEGALSAA-RTASQLIDXRKHKGEHPRXGALDVCPFIPVRGVSXDECVLCAKAF--- 111
Query: 125 IGSGLQGVIVIGSTRWVDNYNIPVF 149
R + N+PV+
Sbjct: 112 ------------GQRLAEELNVPVY 124
>pdb|3ASY|A Chain A, Ligand-Free Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASY|B Chain B, Ligand-Free Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASZ|A Chain A, Cmp-Complex Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASZ|B Chain B, Cmp-Complex Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
Length = 211
Score = 31.2 bits (69), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 129 LQGVIVIGSTRWVDNYNIPVF---STNIAAVRRIAKQVSERGGGLASVQAMVLIRGEDIT 185
L+G++V+ D ++ VF + +RR+ + V ERG L V A L E +
Sbjct: 110 LEGILVLYPKELRDLMDLKVFVDADADERFIRRLKRDVLERGRSLEGVVAQYL---EQVK 166
Query: 186 EVECNLLKPSKIGGD 200
+ + ++P+K D
Sbjct: 167 PMHLHFVEPTKRYAD 181
>pdb|3GQJ|A Chain A, Crystal Structure Of Cell Inhibiting Factor (Cif) From
Photorhabdus Luminescens
Length = 261
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 140 WVDNYNIPVFSTNIAAV-RRIAKQVSERGGGLASVQAMVLIRGEDITEVECNL 191
W DN+ + + ++A + +I + VSE GGL Q MV + D TE C L
Sbjct: 27 WNDNWQDKIINRDLANIFEKIDESVSEL-GGLEMYQEMVGVNPYDPTEPVCGL 78
>pdb|2GNO|A Chain A, Crystal Structure Of A Dna Polymerase Iii, Gamma
Subunit-Related Protein (Tm0771) From Thermotoga
Maritima Msb8 At 2.00 A Resolution
Length = 305
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 29/115 (25%), Positives = 51/115 (44%), Gaps = 9/115 (7%)
Query: 131 GVIVIGSTRWVDNYNIP-----VFSTNIAAVRRIAKQVSERGGGLASVQAMVLIRGEDIT 185
VIV+ + RW +Y +P VF + + V E+ G L + + L+ + T
Sbjct: 113 AVIVLNTRRW--HYLLPTIKSRVFRVVVNVPKEFRDLVKEKIGDLW--EELPLLERDFKT 168
Query: 186 EVECNLLKPSKIGGDKVQVEVDELAAVEGMAVGKGYYTDLSQEEIIERYMKLNSS 240
+E L K+ G ++V E + + KG L+ E++ER+ K+ S
Sbjct: 169 ALEAYKLGAEKLSGLXESLKVLETEKLLKKVLSKGLEGYLACRELLERFSKVESK 223
>pdb|3ERP|A Chain A, Structure Of Idp01002, A Putative Oxidoreductase From And
Essential Gene Of Salmonella Typhimurium
pdb|3ERP|B Chain B, Structure Of Idp01002, A Putative Oxidoreductase From And
Essential Gene Of Salmonella Typhimurium
Length = 353
Score = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 27/50 (54%)
Query: 148 VFSTNIAAVRRIAKQVSERGGGLASVQAMVLIRGEDITEVECNLLKPSKI 197
+ + + VRR+ + + RG L+ + ++R +++T V KPS+I
Sbjct: 276 ITADKLEKVRRLNELAARRGQKLSQMALAWVLRNDNVTSVLIGASKPSQI 325
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.133 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,280,941
Number of Sequences: 62578
Number of extensions: 236715
Number of successful extensions: 608
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 601
Number of HSP's gapped (non-prelim): 10
length of query: 241
length of database: 14,973,337
effective HSP length: 96
effective length of query: 145
effective length of database: 8,965,849
effective search space: 1300048105
effective search space used: 1300048105
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)