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= 003829
(793 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 37.0 bits (84), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 29/47 (61%)
Query: 490 DTFNTLISAYSRCGSFDQAMSIYKRMLEAGVTPDLSTYNAVLAALAR 536
D +N ++ ++R G+F + + + + +AG+TPDL +Y A L + R
Sbjct: 166 DMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGR 212
Score = 36.6 bits (83), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 676 YNTVIFAYCRNGRMKEASRIFSEMRDSGLVPDVITY 711
YN V+ + R G KE + ++D+GL PD+++Y
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSY 203
Score = 35.8 bits (81), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 27/120 (22%), Positives = 55/120 (45%), Gaps = 4/120 (3%)
Query: 352 YNSLISAYARDGLLEEAMELKTQMVEIGITPDVFTYTTLLSGFEKAGKDESAM-KVFEEM 410
YN+++ +AR G +E + + + + G+TPD+ +Y L + +D + + E+M
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQM 227
Query: 411 RSAGCKPNICTFNALIKMHGNRGNFVEMM-KVFDEIN-KCNCKPDIVTWNTLLAVFGQNG 468
G K F A++ +R ++ + KV + P + T L V+ ++G
Sbjct: 228 SQEGLKLQ-ALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDG 286
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 36.6 bits (83), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 24/121 (19%), Positives = 52/121 (42%), Gaps = 9/121 (7%)
Query: 264 MALVEGMKSAGVKPDSYTFNTLISCCRRGSLHEEAA---------GVFEEMKLAGFSPDK 314
+ L + + GV+ Y +N L+ C E++ +F++M + P++
Sbjct: 46 LRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNE 105
Query: 315 VTYNALLDVYGKCRRPKEAMQVLREMKINGCLPSIVTYNSLISAYARDGLLEEAMELKTQ 374
T+ + P+ A ++++MK G P + +Y + + R G ++A E+
Sbjct: 106 ATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAH 165
Query: 375 M 375
M
Sbjct: 166 M 166
Score = 34.7 bits (78), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 33/65 (50%)
Query: 635 TPSLTTYNTLMYMYSRSENFARAEDVLREILAKGIKPDIISYNTVIFAYCRNGRMKEASR 694
P+ T+ + ++ A D+++++ A GI+P + SY +F +CR G +A
Sbjct: 102 VPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYE 161
Query: 695 IFSEM 699
+ + M
Sbjct: 162 VDAHM 166
>pdb|3NF1|A Chain A, Crystal Structure Of The Tpr Domain Of Kinesin Light Chain
1
Length = 311
Score = 35.8 bits (81), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 53/196 (27%), Positives = 83/196 (42%), Gaps = 28/196 (14%)
Query: 349 IVTYNSLISAYARDGLLEEAMELKTQMVE-IGIT-----PDVFTYTTLLSGF---EKAGK 399
+ T ++L+ YA G E A+ L Q +E + T PDV T +L+ + K
Sbjct: 27 LRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYK 86
Query: 400 DES-----AMKVFEEMRSAGCKPNICTFNALIKMHGNRGNFVE---MMKVFDEINK---C 448
D + A+ + E+ T N L ++G RG + E + K EI +
Sbjct: 87 DAANLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLG 146
Query: 449 NCKPDIVTWNTLLAVFGQN-GMDSEVSGVFK---EMKRAGFIPE----RDTFNTLISAYS 500
PD+ LA+ QN G EV ++ E+ + P+ T N L S Y
Sbjct: 147 KDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYL 206
Query: 501 RCGSFDQAMSIYKRML 516
+ G F QA ++YK +L
Sbjct: 207 KQGKFKQAETLYKEIL 222
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 29/60 (48%)
Query: 636 PSLTTYNTLMYMYSRSENFARAEDVLREILAKGIKPDIISYNTVIFAYCRNGRMKEASRI 695
P+ T+ + ++ A D +++ A GI+P + SY +F +CR G +A +
Sbjct: 103 PNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
>pdb|2AUG|A Chain A, Crystal Structure Of The Grb14 Sh2 Domain
pdb|2AUG|B Chain B, Crystal Structure Of The Grb14 Sh2 Domain
Length = 126
Score = 31.2 bits (69), Expect = 2.2, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 82 NRGKPWSHHRLSAKGQQVL---QSLIDDSFDVKDIDS 115
+R +PW HH++S Q L Q L+D F V+D S
Sbjct: 23 HRSQPWFHHKISRDEAQRLIIQQGLVDGVFLVRDSQS 59
>pdb|2HQA|A Chain A, Crystal Structure Of The Catalytic Alpha Subunit Of E.
Coli Replicative Dna Polymerase Iii
Length = 917
Score = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 570 ANGREIDQMLALSEEIYSERAFLELKKKGFSPDIPTLNAMISIYGRRQM-VAKTNEILHF 628
N +D+ +A EE + +R FLEL + G + L+A + + R + V TN++ F
Sbjct: 146 GNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESYLHAAVELAEARGLPVVATNDV-RF 204
Query: 629 MNDSGF 634
++ S F
Sbjct: 205 IDSSDF 210
>pdb|2HNH|A Chain A, Crystal Structure Of The Catalytic Alpha Subunit Of E.
Coli Replicative Dna Polymerase Iii
Length = 910
Score = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 570 ANGREIDQMLALSEEIYSERAFLELKKKGFSPDIPTLNAMISIYGRRQM-VAKTNEILHF 628
N +D+ +A EE + +R FLEL + G + L+A + + R + V TN++ F
Sbjct: 146 GNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESYLHAAVELAEARGLPVVATNDV-RF 204
Query: 629 MNDSGF 634
++ S F
Sbjct: 205 IDSSDF 210
>pdb|1YTD|A Chain A, Crystal Structure Of A Nicotinate
Phosphoribosyltransferase From Thermoplasma Acidophilum,
Native Structure
pdb|1YTE|A Chain A, Crystal Structure Of A Nicotinate
Phosphoribosyltransferase From Thermoplasma Acidophilum,
Phosphoribosylpyrophosphate Bound Structure
pdb|1YTK|A Chain A, Crystal Structure Of A Nicotinate
Phosphoribosyltransferase From Thermoplasma Acidophilum
With Nicotinate Mononucleotide
pdb|2I1O|A Chain A, Crystal Structure Of A Nicotinate
Phosphoribosyltransferase From Thermoplasma Acidophilum
Length = 398
Score = 29.6 bits (65), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%)
Query: 112 DIDSVLSQLLDQNPGEKSEDLGADLLGIVKGLGFHKKTDLALDVFEWFRSCCSKDGNLVL 171
DI ++S LD+N +K + GA+ G+ + K D A+D+ E +K G +
Sbjct: 270 DIKIMVSGGLDENTVKKLREAGAEAFGVGTSISSAKPFDFAMDIVEVNGKPETKRGKMSG 329
Query: 172 RGSVI 176
R +V+
Sbjct: 330 RKNVL 334
>pdb|3OPB|A Chain A, Crystal Structure Of She4p
pdb|3OPB|B Chain B, Crystal Structure Of She4p
Length = 778
Score = 29.6 bits (65), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 47/223 (21%), Positives = 91/223 (40%), Gaps = 44/223 (19%)
Query: 500 SRCGSFDQAMSIYKRMLEAGVTPDLSTYNAVLAALARGGMWEQSEKIFAEMKGGRCKPNE 559
S C +FD+ + TPD+ YN + + + +S K+ P +
Sbjct: 23 SLCAAFDKTLK---------STPDVQKYNDAINTIFQLRQKSESGKM----------PAD 63
Query: 560 LTYSSLLHAYANGREIDQMLALSEEIYSE-RAFLELKKKGFSPDIPTLNAMISIYGRRQM 618
LT S A + ++I+++L S + +SE R L K DIP + I R +
Sbjct: 64 LTNS---EALKDRQKIEEILTRSYQDHSESRVHL---SKLIQNDIPFALNLFEILSRSSI 117
Query: 619 -------------VAKTNEI---LHFMNDSGFTPSLTTYNTLMYMYSRSENFARAEDVLR 662
+A NE+ +H+ D+ T L+ L+ + NF +++
Sbjct: 118 HVFVGCFSNKDATIALLNELQIRIHYGEDTHVTYLLSIILQLLNKFKY--NFKEVRFLVK 175
Query: 663 EILAKGIKPDIISYNTVIFAYCRNGRMKEASRIFSEMRDSGLV 705
E++ + + ++ S +IFA ++ K+ + + S +V
Sbjct: 176 ELILRISEDEVKSMMLIIFAELQSSFQKDFDKAVVDFMSSLIV 218
>pdb|1VFV|A Chain A, Crystal Structure Of The Kif1a Motor Domain Complexed With
Mg-Amppnp
pdb|1VFW|A Chain A, Crystal Structure Of The Kif1a Motor Domain Complexed With
Mg-Amppnp
pdb|1VFX|A Chain A, Crystal Structure Of The Kif1a Motor Domain Complexed With
Adp-mg-alfx
pdb|1VFZ|A Chain A, Crystal Structure Of The Kif1a Motor Domain Complexed With
Adp-Mg-Vo4
pdb|2ZFI|A Chain A, Crystal Structure Of The Kif1a Motor Domain Before Mg
Release
pdb|2ZFJ|A Chain A, Crystal Structure Of The Kif1a Motor Domain During Mg
Release: Mg-Releasing Transition-1
pdb|2ZFK|A Chain A, Crystal Structure Of The Kif1a Motor Domain During Mg
Release: Mg-Releasing Transition-2
pdb|2ZFL|A Chain A, Crystal Structure Of The Kif1a Motor Domain During Mg
Release: Mg-Releasing Transition-3
pdb|2ZFM|A Chain A, Crystal Structure Of The Kif1a Motor Domain After Mg
Release
Length = 366
Score = 29.3 bits (64), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 635 TPSLTTYNTLMYMYSRSE--NFARAEDVLREILAKGIKPDIISYNTVIFAYCRNGRMKEA 692
TP +++ + ++ E N+A + V R+I + ++ YN IFAY + G K
Sbjct: 46 TPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSY 105
Query: 693 SRIFSEMRD-SGLVPDV 708
+ + + +D G++P +
Sbjct: 106 TMMGKQEKDQQGIIPQL 122
>pdb|1I6I|A Chain A, Crystal Structure Of The Kif1a Motor Domain Complexed With
Mg-Amppcp
Length = 366
Score = 29.3 bits (64), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 635 TPSLTTYNTLMYMYSRSE--NFARAEDVLREILAKGIKPDIISYNTVIFAYCRNGRMKEA 692
TP +++ + ++ E N+A + V R+I + ++ YN IFAY + G K
Sbjct: 46 TPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSY 105
Query: 693 SRIFSEMRD-SGLVPDV 708
+ + + +D G++P +
Sbjct: 106 TMMGKQEKDQQGIIPQL 122
>pdb|1IA0|K Chain K, Kif1a Head-Microtubule Complex Structure In Atp-Form
pdb|2HXF|C Chain C, Kif1a Head-Microtubule Complex Structure In Amppnp-Form
pdb|2HXH|C Chain C, Kif1a Head-Microtubule Complex Structure In Adp-Form
Length = 394
Score = 29.3 bits (64), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 635 TPSLTTYNTLMYMYSRSE--NFARAEDVLREILAKGIKPDIISYNTVIFAYCRNGRMKEA 692
TP +++ + ++ E N+A + V R+I + ++ YN IFAY + G K
Sbjct: 62 TPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSY 121
Query: 693 SRIFSEMRD-SGLVPDV 708
+ + + +D G++P +
Sbjct: 122 TMMGKQEKDQQGIIPQL 138
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
0.319 0.134 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,910,038
Number of Sequences: 62578
Number of extensions: 897269
Number of successful extensions: 2388
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2359
Number of HSP's gapped (non-prelim): 39
length of query: 793
length of database: 14,973,337
effective HSP length: 107
effective length of query: 686
effective length of database: 8,277,491
effective search space: 5678358826
effective search space used: 5678358826
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)