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= 005977
(666 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3EC1|A Chain A, Structure Of Yqeh Gtpase From Geobacillus
Stearothermophilus (An Atnos1 ATNOA1 ORTHOLOG)
pdb|3EC1|B Chain B, Structure Of Yqeh Gtpase From Geobacillus
Stearothermophilus (An Atnos1 ATNOA1 ORTHOLOG)
Length = 369
Score = 119 bits (299), Expect = 5e-27, Method: Compositional matrix adjust.
Identities = 83/278 (29%), Positives = 138/278 (49%), Gaps = 13/278 (4%)
Query: 339 GTKVDLLPSQVSPTRLDRWVRHRAKAGGAPKLNGVYLVSARKDLGVRNLLAFIKELAGPR 398
G K DLLP V +L RW+R A+ G ++ V LVSA K +G+ ++ I
Sbjct: 105 GNKADLLPRSVKYPKLLRWMRRMAEELGLCPVD-VCLVSAAKGIGMAKVMEAINRYR-EG 162
Query: 399 GNVWVIGAQNAGKSTLINTFAKKEGVKVSKLTEAPXXXXXXXXXXXXXXXXAKAKLYDTP 458
G+V+V+G N GKST IN ++ K + +T + + A LYDTP
Sbjct: 163 GDVYVVGCTNVGKSTFINRIIEEATGKGNVITTS--YFPGTTLDMIEIPLESGATLYDTP 220
Query: 459 GLLHPHLMSMRLNRDEQKMVEIRKELQPRTYRVKGGQAVHVGGLMRLDLDQASVETIYVT 518
G+++ H M+ ++ + K++ ++E+ PR Y++ GQ + GGL RLD + +
Sbjct: 221 GIINHHQMAHFVDARDLKIITPKREIHPRVYQLNEGQTLFFGGLARLDYIKGGRRSF--V 278
Query: 519 VWASPNVSLHLGKIENADEIWKNHVGIRLQPPIGQDRASELGTWKDRKLKVSGTSWDVNG 578
+ + +++H K+E AD ++ N +G L PP + A+E R L V
Sbjct: 279 CYMANELTVHRTKLEKADSLYANQLGELLSPP-SKRYAAEFPPLVPRSLSVKERK----- 332
Query: 579 IDIAAAGLGWFSLGLKGEASLTLWTYDGIEITLREPLV 616
DI +GLGW + G A L + G+++ +R+ L+
Sbjct: 333 TDIVFSGLGWVTCNDPG-AQLVVHAPKGVDVFIRQSLI 369
>pdb|3H2Y|A Chain A, Crystal Structure Of Yqeh Gtpase From Bacillus Anthracis
With Dgdp Bound
Length = 368
Score = 106 bits (264), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 97/378 (25%), Positives = 162/378 (42%), Gaps = 47/378 (12%)
Query: 244 EVTVCARCHSLRNYGQVKNEVAENLIPDFDFDRVIATRLMKPSGNANAXXXXXXXXXXXX 303
E +C RC L++Y NE+ + + D DF R++ G ++A
Sbjct: 33 EQVICQRCFRLKHY----NEIQDVSLTDDDF-----LRILNGIGKSDALVVKIVDIFDFN 83
Query: 304 XXXXPKRAAKSLFKKLEEAKDDAXXXXXXXXXXXXGTKVDLLPSQVSPTRLDRWVRHRAK 363
P L + + K G K DL+P V ++ W R+ AK
Sbjct: 84 GSWLP-----GLHRFVGNNK-----------VLLVGNKADLIPKSVKHDKVKHWXRYSAK 127
Query: 364 AGGAPKLNGVYLVSARKDLGVRNLLAFIKELAGPRGNVWVIGAQNAGKSTLINTFAKK-- 421
G K V+L+SA K G+ L I+ G + +V+V+G N GKST IN K+
Sbjct: 128 QLGL-KPEDVFLISAAKGQGIAELADAIEYYRGGK-DVYVVGCTNVGKSTFINRXIKEFS 185
Query: 422 -EGVKVSKLTEAPXXXXXXXXXXXXXXXXAKAKLYDTPGLLHPHLMSMRLNRDEQKMVEI 480
E V + P ++ LYDTPG+++ H + + + K++
Sbjct: 186 DETENVITTSHFPGTTLDLIDIPLD----EESSLYDTPGIINHHQXAHYVGKQSLKLITP 241
Query: 481 RKELQPRTYRVKGGQAVHVGGLMRLDLDQASVETIYVTVWASPNVSLHLGKIENADEIWK 540
KE++P +++ Q + GL R D T S +++H K+E ADE++K
Sbjct: 242 TKEIKPXVFQLNEEQTLFFSGLARFDYVSGGRRAF--TCHFSNRLTIHRTKLEKADELYK 299
Query: 541 NHVGIRLQPPIGQDRAS--ELGTWKDRKLKVSGTSWDVNGIDIAAAGLGWFSLGLKGEAS 598
NH G L PP ++ + EL + + ++ T D+ +GLGW ++ G A
Sbjct: 300 NHAGDLLSPPTPEELENXPELVKY-EFNIREPKT-------DVVFSGLGWVTVNEPG-AK 350
Query: 599 LTLWTYDGIEITLREPLV 616
+ G+ ++LR+ L+
Sbjct: 351 IVAHVPKGVSVSLRKSLI 368
>pdb|1PUJ|A Chain A, Structure Of B. Subtilis Ylqf Gtpase
Length = 282
Score = 32.3 bits (72), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 11/72 (15%)
Query: 403 VIGAQNAGKSTLINTFAKKEGVKVSKLTEAPXXXXXXXXXXXXXXXXAKAKLYDTPGLLH 462
+IG N GKSTLIN AKK ++K + P + +L DTPG+L
Sbjct: 125 IIGIPNVGKSTLINRLAKK---NIAKTGDRP----GITTSQQWVKVGKELELLDTPGILW 177
Query: 463 P----HLMSMRL 470
P L+ +RL
Sbjct: 178 PKFEDELVGLRL 189
>pdb|3R9W|A Chain A, Crystal Structure Of Era In Complex With Mggdpnp And
Nucleotides 1506- 1542 Of 16s Ribosomal Rna
pdb|3R9X|A Chain A, Crystal Structure Of Era In Complex With Mggdpnp,
Nucleotides 1506- 1542 Of 16s Ribosomal Rna, And Ksga
Length = 307
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 27/65 (41%), Gaps = 3/65 (4%)
Query: 399 GNVWVIGAQNAGKSTLINTFAKKEGVKVSKLTEAPXXXXXXXXXXXXXXXXAKAKLYDTP 458
G V ++G N GKSTL+N G KVS ++ A+ DTP
Sbjct: 10 GYVAIVGKPNVGKSTLLNNLL---GTKVSIISPKAGTTRMRVLGVKNIPNEAQIIFLDTP 66
Query: 459 GLLHP 463
G+ P
Sbjct: 67 GIYEP 71
>pdb|3IEV|A Chain A, Crystal Structure Of Era In Complex With Mggnp And The 3'
End Of 16s Rrna
Length = 308
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 27/65 (41%), Gaps = 3/65 (4%)
Query: 399 GNVWVIGAQNAGKSTLINTFAKKEGVKVSKLTEAPXXXXXXXXXXXXXXXXAKAKLYDTP 458
G V ++G N GKSTL+N G KVS ++ A+ DTP
Sbjct: 11 GYVAIVGKPNVGKSTLLNNLL---GTKVSIISPKAGTTRMRVLGVKNIPNEAQIIFLDTP 67
Query: 459 GLLHP 463
G+ P
Sbjct: 68 GIYEP 72
>pdb|3CNL|A Chain A, Crystal Structure Of Gnp-Bound Ylqf From T. Maritima
pdb|3CNN|A Chain A, Gtp-Bound Structure Of Tm Ylqf
pdb|3CNO|A Chain A, Gdp-Bound Structue Of Tm Ylqf
Length = 262
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 389 AFIKELAGPR-GNVWVIGAQNAGKSTLINTFAKKEGVKVSKLTEAPXXXXXXXXXXXXXX 447
+K+L+ R V ++G N GKST+IN K +G + S + P
Sbjct: 89 VLLKKLSFDRLARVLIVGVPNTGKSTIIN---KLKGKRASSVGAQPGITKGIQWFSLENG 145
Query: 448 XXAKAKLYDTPGLLHPHLMS 467
K+ DTPG+L+ ++ S
Sbjct: 146 ----VKILDTPGILYKNIFS 161
>pdb|3O0L|A Chain A, Crystal Structure Of A Pfam Duf1425 Family Member
(Shew_1734) From Shewanella Sp. Pv-4 At 1.81 A
Resolution
pdb|3O0L|B Chain B, Crystal Structure Of A Pfam Duf1425 Family Member
(Shew_1734) From Shewanella Sp. Pv-4 At 1.81 A
Resolution
Length = 112
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 563 KDRKLKVSGTSWDVNGIDIAAAGLGWFSLGLKGE 596
KD++L+ T +D+NG + G+ W SL L G+
Sbjct: 52 KDQRLQYKFTWYDINGATVEDEGVSWKSLKLHGK 85
>pdb|1WF3|A Chain A, Crystal Structure Of Gtp-Binding Protein Tt1341 From
Thermus Thermophilus Hb8
Length = 301
Score = 28.9 bits (63), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 28/65 (43%), Gaps = 4/65 (6%)
Query: 399 GNVWVIGAQNAGKSTLINTFAKKEGVKVSKLTEAPXXXXXXXXXXXXXXXXAKAKLYDTP 458
G V ++G N GKSTL+N GVKV+ ++ P + DTP
Sbjct: 8 GFVAIVGKPNVGKSTLLNNLL---GVKVAPISPRPQTTRKRLRGILTEGRR-QIVFVDTP 63
Query: 459 GLLHP 463
GL P
Sbjct: 64 GLHKP 68
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 0.136 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,832,798
Number of Sequences: 62578
Number of extensions: 579113
Number of successful extensions: 1360
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1343
Number of HSP's gapped (non-prelim): 18
length of query: 666
length of database: 14,973,337
effective HSP length: 105
effective length of query: 561
effective length of database: 8,402,647
effective search space: 4713884967
effective search space used: 4713884967
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)