Alignments for a candidate for gltX in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for gltX in Burkholderia phytofirmans PsJN

Align Glutamate--tRNA ligase; EC 6.1.1.17 (characterized, see rationale)
to candidate BPHYT_RS12355 BPHYT_RS12355 glutamate--tRNA ligase

Query= uniprot:A0A0H3C8P5_CAUVN
         (470 letters)



>FitnessBrowser__BFirm:BPHYT_RS12355
          Length = 469

 Score =  337 bits (863), Expect = 7e-97
 Identities = 189/469 (40%), Positives = 267/469 (56%), Gaps = 12/469 (2%)

Query: 7   TGVVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEG 66
           T V TRFAPSPTGF+H+G  R+AL+ W +AR   G F++R+EDTD ERST  +V AI EG
Sbjct: 3   TSVRTRFAPSPTGFIHLGNIRSALYPWAFARKMKGTFVLRIEDTDVERSTSESVDAILEG 62

Query: 67  LDWLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR 126
           + WLGL  D+   +Q  R  R+ EV+ ++   G  Y C+MS EEL+  RE+ R  G   R
Sbjct: 63  MAWLGLDFDEGPFYQMQRMDRYREVLKQMQDAGLVYPCYMSTEELDALRERQREAGEKPR 122

Query: 127 --SPWRDAPEGDLSAPH-----VIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRAD 179
               WR  P   L  P      V+RF+ PL G    +D VKG +   N ELDDLV+ R D
Sbjct: 123 YDGTWRPEPGKVLPEPPAGVQPVLRFRNPLTGVVAWDDAVKGRIEISNEELDDLVIARPD 182

Query: 180 GAPTYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGA 239
           G PTYN  VVVDD DM +THVIRGDDH+NN  RQ  I +A+    P +AH+P +    G 
Sbjct: 183 GTPTYNFCVVVDDLDMRITHVIRGDDHVNNTPRQINILRALGGEPPVYAHLPTVLNEQGE 242

Query: 240 KLSKRHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPA 299
           K+SKRHGA +V  + D G++PE + NYLARLGW HGD E+F+ EQ + WFD+  + K+PA
Sbjct: 243 KMSKRHGAMSVVGYRDAGFLPEAVVNYLARLGWSHGDAEIFSREQFVEWFDLEHLGKSPA 302

Query: 300 RLDWAKLNHINAQHLRKADDARLTALALAAAETRG--EPLPADAAERIARTVPEVKEGAK 357
           + D  KL  +NA ++++AD+ARL  LA       G  E   A  A+ +A  V  +K+ A 
Sbjct: 303 QYDHDKLAWLNAHYIKEADNARLAELAKPFFAELGIDEAALAQGAD-LAAVVGLLKDRAS 361

Query: 358 TILELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKS 417
           T+ E+ ++ A   +T P    E   + +T+     L  L   L    ++    +   LK+
Sbjct: 362 TVKEIAENAAMFYRT-PAPDAESLAQHVTDVVRPALADLAAALKTV-EWTKEAIAAALKA 419

Query: 418 FAESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466
              +  +   +    +R ++ G    P ++  +    RD  +GR++ AL
Sbjct: 420 TLGAHKLKMPQLAMPVRLLVAGTTHTPSIDSVLMLFGRDVVVGRIEKAL 468


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: 611
Number of extensions: 33
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: 469
Length adjustment: 33
Effective length of query: 437
Effective length of database: 436
Effective search space:   190532
Effective search space used:   190532
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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

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

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, the paper from 2022 on GapMind for carbon sources, 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

GapMind for Amino acid biosynthesis