GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Shewanella halifaxensis HAW-EB4

Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate WP_012277641.1 SHAL_RS13305 aldehyde dehydrogenase (NADP(+))

Query= metacyc::G1G01-1343-MONOMER
         (525 letters)



>NCBI__GCF_000019185.1:WP_012277641.1
          Length = 521

 Score =  425 bits (1092), Expect = e-123
 Identities = 232/487 (47%), Positives = 308/487 (63%), Gaps = 3/487 (0%)

Query: 25  DPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRETSLEQRAEFLEAIATQIEALGDAL 84
           +P T + L   +   +   VA A A A  AF  YR  +  +RAEFLEAIA +I+A   A+
Sbjct: 30  NPVTNEALSFRFANASKTIVASAAAAAKQAFVQYRSLAPTRRAEFLEAIADEIQADIVAI 89

Query: 85  IDRAVIETGLPKARIQGERGRTCTQLRTFARTVRAGEWLDVR-IDSALPERQPLPRADLR 143
            + A +ETGLP AR+QGE GRTC QLR FA  +R    +D R +D A P RQPLP+ + R
Sbjct: 90  TETAHLETGLPMARLQGETGRTCGQLRLFAGNLRNP--IDSRYVDLANPARQPLPKPETR 147

Query: 144 QRQVALGPVAVFGASNFPLAFSVAGGDTASALAAGCPVVVKAHSAHPGTSELVGQAVAQA 203
              + LGPVAVFGASNFPLAFS AGGDTASALAAGC +VVK H AH  TSELV +A+ +A
Sbjct: 148 LTTLPLGPVAVFGASNFPLAFSTAGGDTASALAAGCTIVVKGHPAHAATSELVSRAIERA 207

Query: 204 VKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFTGSRSGGMALCQAAQARPEPIPVY 263
             +C +P GVF+L+ G   EV   LV+ P IKAVGFTGS   G  L     AR EPIP Y
Sbjct: 208 AVKCDMPNGVFNLVQGCAPEVSTQLVTTPAIKAVGFTGSLKVGRILSDLCAARAEPIPFY 267

Query: 264 AEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQFCTNPGLVIARQGPALQRFITAA 323
            E+ SINP F+    L  +AE+LA   V S+  G GQFCT+PG+++A +G AL R+    
Sbjct: 268 GELGSINPQFILANILDEQAESLATTQVQSMLMGHGQFCTSPGVIVAVKGDALNRYKATL 327

Query: 324 AGYVQQGAAQTMLTPGIFSAYQAGIAALADNPHAQAITSGQAGQGPNQCQAQLFVTQAEA 383
           A  +   +A +ML+ GI + YQA I  L  +P  + I  G++    +  +       A  
Sbjct: 328 AQDIASQSAASMLSAGIAANYQAQIETLLADPKVELIAQGESSPANHFTRPMALKVTATE 387

Query: 384 FLADPALQAEVFGAASLVVACTDDEQVRQVAEHLEGQLTATLQLDEADIDSARALLPTLE 443
           F+A  A+Q EVFG  +++V C D  Q++ +AE LEGQLTAT+     ++     L+  + 
Sbjct: 388 FIASNAIQQEVFGPCAVLVECDDSAQMQSIAEQLEGQLTATVHGLVPELTENTTLIEAIA 447

Query: 444 RKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTSVGTAAILRFLRPVCYQDVPDALL 503
              GR++ N  PTGVEVC +M HGGP+PA++D+RTTSVG+AA+ RF RP+CYQ++P ALL
Sbjct: 448 FNVGRLIFNQMPTGVEVCHSMNHGGPYPASTDSRTTSVGSAAMERFERPICYQNMPQALL 507

Query: 504 PQALKHG 510
           P  ++ G
Sbjct: 508 PTRVQEG 514


Lambda     K      H
   0.319    0.134    0.391 

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: 680
Number of extensions: 24
Number of successful extensions: 2
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: 525
Length of database: 521
Length adjustment: 35
Effective length of query: 490
Effective length of database: 486
Effective search space:   238140
Effective search space used:   238140
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: 52 (24.6 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