GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Paraburkholderia bryophila 376MFSha3.1

Align Glutamate--tRNA ligase; EC 6.1.1.17 (characterized, see rationale)
to candidate H281DRAFT_00567 H281DRAFT_00567 glutamyl-tRNA synthetase

Query= uniprot:A0A0H3C8P5_CAUVN
         (470 letters)



>FitnessBrowser__Burk376:H281DRAFT_00567
          Length = 469

 Score =  341 bits (874), Expect = 4e-98
 Identities = 189/470 (40%), Positives = 268/470 (57%), Gaps = 12/470 (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  MEWLGLDFDEGPYYQMQRMDRYREVLKQMQDAGLVYPCYMSTEELDALRERQREAGEKPR 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 GTPTYNFCVVVDDLDMRITHVIRGDDHVNNTPRQINILRALGGETPVYAHLPTVLNEQGE 242

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

Query: 300 RLDWAKLNHINAQHLRKADDARLTALALAAAETRG--EPLPADAAERIARTVPEVKEGAK 357
           + D  KLN +NA ++++AD+ RL  LA       G  E   A  A+ +   V  +K+ A 
Sbjct: 303 QYDHDKLNWLNAHYIKEADNGRLAGLARPFLAELGIDEATIAQGAD-LTAVVGLLKDRAS 361

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

Query: 418 FAESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDALA 467
              +  +   +    +R ++ G    P ++  +    RD  +GR++ ALA
Sbjct: 420 TLGTHKLKMPQLAMPVRLLVAGTTHTPSIDMVLMLFGRDVVVGRIEKALA 469


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: 613
Number of extensions: 29
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:

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. 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:

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:

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