GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cola:Echvi_2790
          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.

Links

Downloads

Related tools

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