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= 046621
(213 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FU3|A Chain A, Cid Of Human Rprd1b
pdb|4FU3|B Chain B, Cid Of Human Rprd1b
Length = 135
Score = 117 bits (294), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 56/116 (48%), Positives = 78/116 (67%)
Query: 5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
+F L +KLS+L+NSQQS+++LS W I HRK A IV W + ++ ++++FLYL
Sbjct: 3 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL 62
Query: 65 ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120
AND++QNS+RKG EF EF VL A HV DE KK + RL++IW+ER V+G
Sbjct: 63 ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYG 118
>pdb|4HFG|A Chain A, Cid Of Human Rprd1b
pdb|4HFG|B Chain B, Cid Of Human Rprd1b
Length = 135
Score = 116 bits (290), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 60/133 (45%), Positives = 82/133 (61%), Gaps = 1/133 (0%)
Query: 5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
+F L +KLS+L+NSQ S+++LS W I HRK A IV W + ++ ++++FLYL
Sbjct: 3 SFSESALEKKLSELSNSQHSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL 62
Query: 65 ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG- 123
AND++QNS+RKG EF EF VL A HV DE KK + RL++IW+ER V+G
Sbjct: 63 ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI 122
Query: 124 QGLKDEMLGKNPP 136
Q LK M P
Sbjct: 123 QQLKLSMEDSKSP 135
>pdb|4FLB|A Chain A, Cid Of Human Rprd2
Length = 132
Score = 73.6 bits (179), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 42/110 (38%), Positives = 58/110 (52%), Gaps = 4/110 (3%)
Query: 11 LSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQ 70
L K + N+ +SI+ LS WCI ++K IV W K S R++ YLAND++Q
Sbjct: 10 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQ 69
Query: 71 NSRRKGSEFVNE-FWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVF 119
N +RK + E F VLP A V D K+V R+ IWE+R V+
Sbjct: 70 NCKRKNAIIFRESFADVLPEAAALVKDPS---VSKSVERIFKIWEDRNVY 116
>pdb|2KM4|A Chain A, Solution Structure Of Rtt103 Ctd Interacting Domain
pdb|2L0I|A Chain A, Solution Structure Of Rtt103 Ctd-Interacting Domain Bound
To A Ser2 Phosphorylated Ctd Peptide
Length = 142
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 35/119 (29%), Positives = 63/119 (52%), Gaps = 3/119 (2%)
Query: 5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSF--NSSQKEQRVSFL 62
AF + + KL+ L +SQ+SI S S+W + + A ++ E W + S +++ L
Sbjct: 2 AFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGL 61
Query: 63 YLANDILQNSR-RKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120
YL N ++Q ++ +K +F + F KV L + KK ++R+V+I +ER +F
Sbjct: 62 YLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQEFPRDLKKKLSRVVNILKERNIFS 120
>pdb|3HL2|A Chain A, The Crystal Structure Of The Human Sepsecs-Trnasec Complex
pdb|3HL2|B Chain B, The Crystal Structure Of The Human Sepsecs-Trnasec Complex
pdb|3HL2|C Chain C, The Crystal Structure Of The Human Sepsecs-Trnasec Complex
pdb|3HL2|D Chain D, The Crystal Structure Of The Human Sepsecs-Trnasec Complex
Length = 501
Score = 30.8 bits (68), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 12/73 (16%)
Query: 55 KEQRVSFLYLANDILQNSRRKGSEFVNEFWKVL-----PAALKHVYDNGDEYGKKAVTRL 109
KE++ F YL+N I +K SE NE ++L P +L DE+ KAVT+L
Sbjct: 339 KERKEMFSYLSNQI-----KKLSEAYNE--RLLHTPHNPISLAMTLKTLDEHRDKAVTQL 391
Query: 110 VDIWEERKVFGSR 122
+ R+V G+R
Sbjct: 392 GSMLFTRQVSGAR 404
>pdb|1H41|A Chain A, Pseudomonas Cellulosa E292a Alpha-D-Glucuronidase Mutant
Complexed With Aldotriuronic Acid
pdb|1H41|B Chain B, Pseudomonas Cellulosa E292a Alpha-D-Glucuronidase Mutant
Complexed With Aldotriuronic Acid
Length = 708
Score = 27.3 bits (59), Expect = 6.1, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 10/81 (12%)
Query: 22 QQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVN 81
Q S + R H+ A + W + S+Q +F+ ++ SR G + +
Sbjct: 456 QSSWYAFGRMAWDHQISAATAADEWLRMTFSNQP----AFIEPVKQMMLVSREAGVNYRS 511
Query: 82 EFWKVLPAALKHVYDNGDEYG 102
P L H+Y GD YG
Sbjct: 512 ------PLGLTHLYSQGDHYG 526
>pdb|1GQI|A Chain A, Structure Of Pseudomonas Cellulosa Alpha-D-Glucuronidase
pdb|1GQI|B Chain B, Structure Of Pseudomonas Cellulosa Alpha-D-Glucuronidase
pdb|1GQJ|A Chain A, Structure Of Pseudomonas Cellulosa Alpha-D-Glucuronidase
Complexed With Xylobiose
pdb|1GQJ|B Chain B, Structure Of Pseudomonas Cellulosa Alpha-D-Glucuronidase
Complexed With Xylobiose
pdb|1GQK|A Chain A, Structure Of Pseudomonas Cellulosa Alpha-D-Glucuronidase
Complexed With Glucuronic Acid
pdb|1GQK|B Chain B, Structure Of Pseudomonas Cellulosa Alpha-D-Glucuronidase
Complexed With Glucuronic Acid
pdb|1GQL|A Chain A, Structure Of Pseudomonas Cellulosa Alpha-D-Glucuronidase
Complexed With Glucuronic Acid And Xylotriose
pdb|1GQL|B Chain B, Structure Of Pseudomonas Cellulosa Alpha-D-Glucuronidase
Complexed With Glucuronic Acid And Xylotriose
Length = 708
Score = 27.3 bits (59), Expect = 6.5, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 10/81 (12%)
Query: 22 QQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVN 81
Q S + R H+ A + W + S+Q +F+ ++ SR G + +
Sbjct: 456 QSSWYAFGRMAWDHQISAATAADEWLRMTFSNQP----AFIEPVKQMMLVSREAGVNYRS 511
Query: 82 EFWKVLPAALKHVYDNGDEYG 102
P L H+Y GD YG
Sbjct: 512 ------PLGLTHLYSQGDHYG 526
>pdb|3BVE|A Chain A, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVE|B Chain B, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVE|C Chain C, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVE|D Chain D, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVE|E Chain E, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVE|F Chain F, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVF|A Chain A, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVF|B Chain B, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVF|C Chain C, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVF|D Chain D, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVF|E Chain E, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVF|F Chain F, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVI|A Chain A, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVI|B Chain B, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVI|C Chain C, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVI|D Chain D, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVI|E Chain E, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVI|F Chain F, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVK|A Chain A, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVK|B Chain B, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVK|C Chain C, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVK|D Chain D, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVK|E Chain E, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVK|F Chain F, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVL|A Chain A, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVL|B Chain B, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVL|C Chain C, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVL|D Chain D, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVL|E Chain E, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
pdb|3BVL|F Chain F, Structural Basis For The Iron Uptake Mechanism Of
Helicobacter Pylori Ferritin
Length = 181
Score = 26.9 bits (58), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 9 QILSEKLSKLNNSQQSIESLSRWCITH 35
++L+E+++K NS S+S WC TH
Sbjct: 22 KLLNEQVNKEMNSSNLYMSMSSWCYTH 48
>pdb|3EGM|A Chain A, Structural Basis Of Iron Transport Gating In
Helicobacter Pylori Ferritin
pdb|3EGM|B Chain B, Structural Basis Of Iron Transport Gating In
Helicobacter Pylori Ferritin
pdb|3EGM|C Chain C, Structural Basis Of Iron Transport Gating In
Helicobacter Pylori Ferritin
pdb|3EGM|D Chain D, Structural Basis Of Iron Transport Gating In
Helicobacter Pylori Ferritin
pdb|3EGM|E Chain E, Structural Basis Of Iron Transport Gating In
Helicobacter Pylori Ferritin
pdb|3EGM|F Chain F, Structural Basis Of Iron Transport Gating In
Helicobacter Pylori Ferritin
Length = 181
Score = 26.9 bits (58), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 9 QILSEKLSKLNNSQQSIESLSRWCITH 35
++L+E+++K NS S+S WC TH
Sbjct: 22 KLLNEQVNKEMNSSNLYMSMSSWCYTH 48
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
0.312 0.128 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,414,477
Number of Sequences: 62578
Number of extensions: 254588
Number of successful extensions: 492
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 480
Number of HSP's gapped (non-prelim): 15
length of query: 213
length of database: 14,973,337
effective HSP length: 95
effective length of query: 118
effective length of database: 9,028,427
effective search space: 1065354386
effective search space used: 1065354386
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)