GapMind for Amino acid biosynthesis

 

Aligments for a candidate for gltX in Desulfovibrio vulgaris Miyazaki F

Align Glutamate--tRNA ligase; EC 6.1.1.17 (characterized, see rationale)
to candidate 8500239 DvMF_0996 glutamyl-tRNA synthetase (RefSeq)

Query= uniprot:A0A0H3C8P5_CAUVN
         (470 letters)



>lcl|FitnessBrowser__Miya:8500239 DvMF_0996 glutamyl-tRNA synthetase
           (RefSeq)
          Length = 464

 Score =  360 bits (925), Expect = e-104
 Identities = 208/465 (44%), Positives = 266/465 (57%), Gaps = 8/465 (1%)

Query: 7   TGVVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEG 66
           T VVTRFAPSPTG LHIGGARTA+FNWL ARH GG FL+R+EDTD+ERS +    +I   
Sbjct: 2   TKVVTRFAPSPTGHLHIGGARTAIFNWLLARHFGGTFLLRIEDTDQERSLQEYTDSILAS 61

Query: 67  LDWLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR 126
           + WLGL  D ++I+Q  R   +   +  +L  G AY C  + EE+E  RE AR  G   +
Sbjct: 62  MRWLGLDWDGDLIYQSRRFDIYNGYIDRMLETGHAYWCECTPEEVEQMRETARERGLKPK 121

Query: 127 SPWRDAPEGDLSAP-HVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTYN 185
              R    G    P  V+R K PL G  +  D+VKG + F   ELDD+VL R+DG PTYN
Sbjct: 122 YDGRCRERGLGPGPGRVVRLKAPLTGRVVFEDVVKGTLAFDAAELDDMVLRRSDGTPTYN 181

Query: 186 LAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKRH 245
           +AVVVDD  MGVTHV+RGDDH++N  +Q LIYQA+   +P F H+P+I GPD  KLSKRH
Sbjct: 182 MAVVVDDATMGVTHVLRGDDHVSNTPKQVLIYQALGLPLPIFGHVPMILGPDKKKLSKRH 241

Query: 246 GAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWAK 305
           GA+AV E+   G +P+ + NYL RLGW  GD E+F  ++ +  F   ++  APA  D  K
Sbjct: 242 GARAVIEYEQDGLLPQALVNYLVRLGWSFGDQEIFALQELVEKFTTDNLNSAPAAFDPDK 301

Query: 306 LNHINAQHLRKADDARLTALALAAAETRGEPLPADAAERIARTVPEVKEGAKTILELVDH 365
           L  +NA +LR+     L  LA    +  G  +   A ER+A  VP  +E A  + +L   
Sbjct: 302 LQWLNAHYLRETPVDELARLAAPFVKAEGFDV---APERLATLVPLFRERASNLADLARV 358

Query: 366 CAFALKTRPLALEE---KTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAESE 422
             F L     ALE       K LT E    +  LR  L  A  FD A LE V+  + E  
Sbjct: 359 MRFML-VDATALEHDPAAVAKALTAEGKAHVAALRGLLEQADPFDKAALEKVVHDYVEQG 417

Query: 423 GVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDALA 467
           G+ F + GP LR  L G    P L + M  L R E + RLD A A
Sbjct: 418 GLKFKQVGPPLRVALAGSLGGPGLPEIMEVLGRAETLARLDRAAA 462


Lambda     K      H
   0.319    0.135    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 675
Number of extensions: 37
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 470
Length of database: 464
Length adjustment: 33
Effective length of query: 437
Effective length of database: 431
Effective search space:   188347
Effective search space used:   188347
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory