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

GapMind for catabolism of small carbon sources

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

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate Echvi_2790 Echvi_2790 adenosylmethionine-8-amino-7-oxononanoate transaminase

Query= reanno::pseudo5_N2C3_1:AO356_13150
         (454 letters)



>lcl|FitnessBrowser__Cola:Echvi_2790 Echvi_2790
           adenosylmethionine-8-amino-7-oxononanoate transaminase
          Length = 434

 Score =  192 bits (488), Expect = 2e-53
 Identities = 130/409 (31%), Positives = 206/409 (50%), Gaps = 29/409 (7%)

Query: 36  IITHAKGVYLWDSEGNKILDGMAGLWCVAVGYGREELADAASQQMRELPYYNLFFQTAHP 95
           ++  A GV+L   +G +++DGM+  W    GY    L  A  QQ+  + +  +F    H 
Sbjct: 29  VVKKASGVFLELEDGTRLIDGMSSWWSTIHGYQVPALNRAIQQQLENMAHV-MFGGITHR 87

Query: 96  PVLELSKAIADIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQPNKKVIISRKNGYH 155
           P  EL++A+ ++ P+G+ HVF++ SGS   +  ++M   YW  KGQ +K    + ++GYH
Sbjct: 88  PAAELTQALLEVVPQGLKHVFYSDSGSVAVEVAMKMALQYWHSKGQGSKNRFATVRSGYH 147

Query: 156 GSTVAGASL-GGMTYMHEQGDLPIPGIVHIAQPYWFGEGGDMSPEEFGVWAANQLEEKIL 214
           G T    S+   +T MH   +  +   + +  P     G  + PEE       +  E++L
Sbjct: 148 GDTWHDMSVCDPVTGMHSIFNNRLSPQIFLPAPQSTFHG-QLIPEEL------EEVERVL 200

Query: 215 EIGVDNVGAFIAEPI-QGAGGVIVPPDSYWPRMKEILAKYDILFVADEVICGFGRTGEWF 273
               + + AFI EPI QGAGG+      Y   +K    KYDIL +ADE+  GFGRTG+ F
Sbjct: 201 SSHHEEIAAFILEPIVQGAGGMRFYHPDYLNSLKTHCEKYDILLIADEIATGFGRTGKLF 260

Query: 274 GTDHYGLKPHMMTIAKGLTSGYIPMGGLIVRDDVVAVLNEG--GDFNHGFTYSGHPVAAA 331
             +H  + P +M I K LT GY+     +   DV   +++G  G F HG T+ G+P+A A
Sbjct: 261 ACEHAAITPDIMCIGKALTGGYMSFAATLCTADVAHTISDGSPGVFMHGPTFMGNPLACA 320

Query: 332 VALENIRIL--RDEKI-IERVHSETAPYLQKRLRELNDHPLVGEVRGVGLLGAIELVQDK 388
            AL ++ +L  +D K  I+ + S    +L   L  L     V EVR +G +G +E+    
Sbjct: 321 TALASLELLLAKDWKAEIQAIES----HLNDALAGLQTLEAVKEVRVLGAIGVVEM---- 372

Query: 389 ATRKRYEGKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVISKAEIDEL 437
             +   + K +     +     GL +R  G  +   PP VI+ AE+ +L
Sbjct: 373 --KAEVDMKAIQAALTK----RGLWLRPFGKLIYTMPPFVITPAELQQL 415


Lambda     K      H
   0.320    0.139    0.431 

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: 491
Number of extensions: 30
Number of successful extensions: 6
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: 454
Length of database: 434
Length adjustment: 32
Effective length of query: 422
Effective length of database: 402
Effective search space:   169644
Effective search space used:   169644
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 (21.8 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:

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 preprint on GapMind for carbon sources, or view the source code.

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 catabolism of small carbon sources