GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Echinicola vietnamensis KMM 6221, DSM 17526

Align Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized)
to candidate Echvi_0577 Echvi_0577 ornithine aminotransferase

Query= curated2:P94427
         (436 letters)



>FitnessBrowser__Cola:Echvi_0577
          Length = 413

 Score =  199 bits (506), Expect = 1e-55
 Identities = 125/408 (30%), Positives = 215/408 (52%), Gaps = 45/408 (11%)

Query: 35  KGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKRQAEELI--HPGFNVMMYPTY 92
           +GEG  ++D++G ++ DF  +   +N GH HP++++ +  QA  L      F+  +   +
Sbjct: 32  RGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPRILQTLIDQAGTLTLTSRAFHNDVLGPF 91

Query: 93  IELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKY-------TKRQGVVSFTRG-F 144
            +   +  G        K + +N+GAE VE A+KIARK+        + +G +   +  F
Sbjct: 92  EKFLTEYFGY------DKVLPMNTGAEGVETAIKIARKWGYEKKGIPENEGTIIVAKNNF 145

Query: 145 HGRTNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDDMVIQAFNDFF 204
           HGRT   +S ++     K  FGP+ P     P               +DD  I A  D  
Sbjct: 146 HGRTTTVISFSNDETARK-NFGPYTPGFVTIP---------------HDD--IDALKDVL 187

Query: 205 IASVAPETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEIQTGFARTGTY 264
             S   + +   ++EP+QGE G  +P + +++ VA+ CK+HG++F+ADEIQTG ARTG  
Sbjct: 188 SQS---KNIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIARTGKL 244

Query: 265 FAIEHFDVVPDLITVSKSLAAGL-PLSGVIGRAEMLDAAAPGELGGTYAGSPLGCAAALA 323
            A +H  V PD++ + K+++ G  P+S V+    +++   PG+ G T+ G+PLG   A+ 
Sbjct: 245 LACDHEGVKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAKVAMT 304

Query: 324 VLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRRLGAMAAIEIVKDPDTREPDK 383
            L+++++E L E ++++GK+  ++  +   +   +  +R  G + AI I    DT + D 
Sbjct: 305 ALNVVKDEKLAENADKLGKLFRERIQQLVDKSDLVELVRGKGLLNAIVI---NDTEDSDT 361

Query: 384 TKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLSILE 431
                +A    +NG  LL    +GNIIRF  PLVI++  L++   I+E
Sbjct: 362 AWRLCLA--LKENG--LLAKPTHGNIIRFAPPLVITEEQLHDCCDIIE 405


Lambda     K      H
   0.319    0.136    0.393 

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: 473
Number of extensions: 23
Number of successful extensions: 5
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: 436
Length of database: 413
Length adjustment: 32
Effective length of query: 404
Effective length of database: 381
Effective search space:   153924
Effective search space used:   153924
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 Sep 17 2021. The underlying query database was built on Sep 17 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