GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Halioglobus japonicus S1-36

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 WP_084199387.1 C0029_RS09770 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= curated2:P94427
         (436 letters)



>NCBI__GCF_002869505.1:WP_084199387.1
          Length = 467

 Score =  216 bits (549), Expect = 2e-60
 Identities = 139/420 (33%), Positives = 216/420 (51%), Gaps = 15/420 (3%)

Query: 22  SKGVSNGNRSLAVKGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKRQAEELIH 81
           SKG     + +  + EG  ++DLDG ++IDF     T  +G+ HP+++EAV     +   
Sbjct: 36  SKGYVPPAQFIVGRAEGDYVWDLDGNQYIDFQNGWATNPLGNCHPEILEAVHEAQRQY-- 93

Query: 82  PGFNVMMYPTYIELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKYTKRQGVVSFT 141
            GF    +P  I LAE+L  I P     +  F  SG EA E+A+ +A  +T+R+ +VSFT
Sbjct: 94  -GFQ-WEHPLRIPLAERLASIMPSGSLPRFSFEVSGTEAAESAIHLALCHTQRRYIVSFT 151

Query: 142 RGFHGR---TNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDDMVIQ 198
             FHG    T M  +  S    Y  G+   A  V +APFPY  + PAGM    Y +  + 
Sbjct: 152 SCFHGEGLGTKMVSAYNSDNNLYMEGW---AGGVLKAPFPYSEEIPAGMDQAQYTEYCLW 208

Query: 199 AFNDFFIASVAP-ETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEIQTG 257
                    V P E +A +++EP   EGG  IPSK F+Q +   C +   + +ADE+ TG
Sbjct: 209 YIETHLTEYVVPAENIAAILVEPGLAEGGNWIPSKAFMQGLRRICDKFDWLLIADEVLTG 268

Query: 258 FARTGTYFAIEHFDVVPDLITVSKSLAAGL-PLSGVIGRAEMLDAAAPGELGGTYAGSPL 316
             RTGT +A+EHFDVVPD++   K+L+ G+ P +GV  R E+L        G T+AG+P 
Sbjct: 269 LGRTGTMWAVEHFDVVPDILVAGKNLSGGIEPCAGVAARDEILGDNPRATAGSTFAGTPG 328

Query: 317 GCAAALAVLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRRLGAMAAIEIVKDP 376
           GCAAAL  L+I E + +   ++ +  +   +  +W+  +  +  +R LG +  +      
Sbjct: 329 GCAAALKTLEIYERDAVLTHTQHLAGVAMQRMSDWESRYEIVSQVRGLGLLLGVSFRAGR 388

Query: 377 DTREPDKTKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLSILEAGLRA 436
           +  E D   A ++     + GL  +    N   +R    L +++ +L EGLS +E  + A
Sbjct: 389 EDIE-DFHIARSVRDEMLKRGLWAICD--NEPQVRMYPALNMAEDVLLEGLSRMEEAIEA 445


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: 467
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: 467
Length adjustment: 33
Effective length of query: 403
Effective length of database: 434
Effective search space:   174902
Effective search space used:   174902
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 24 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