GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Shewanella loihica PV-4

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 5210422 Shew_2863 short-chain dehydrogenase/reductase SDR (RefSeq)

Query= reanno::pseudo1_N1B4:Pf1N1B4_412
         (272 letters)



>FitnessBrowser__PV4:5210422
          Length = 248

 Score =  141 bits (356), Expect = 1e-38
 Identities = 87/251 (34%), Positives = 136/251 (54%), Gaps = 9/251 (3%)

Query: 20  KNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKADV 79
           + KVVL+TGAA G G+ +    A Q A+LV+ DI    ++ + +   E G   V ++ DV
Sbjct: 6   EGKVVLITGAASGFGKLLAQRLAPQGAKLVLGDINDTALDALCS---ELGECAVGLRCDV 62

Query: 80  SRQQDLHAMARLAIELHGRIDVLVNCAGVNV-FRDPLQMTEEDWHRCFAIDLDGAWYGCK 138
           S + +  A+A+LA E  GR+D+ +N AG++   +  L  TE D    FAI+  G ++G K
Sbjct: 63  SIEAEQLALAQLAEESFGRLDIAINNAGISAPMKSLLATTEADMDLSFAINTKGVFFGMK 122

Query: 139 AVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNAI 198
           A +P M +   G+I+N+AS    +  P   PY  AKH ++G+TR   +E+A +GI+VNAI
Sbjct: 123 AQIPLMQKHKCGAILNVASMAGINGAPKLTPYVAAKHAVVGITRTAALEFAAQGIQVNAI 182

Query: 199 APGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINAS 258
            P +  T +  +      DP    Q    + P RR+  P EV    + + + +  F+   
Sbjct: 183 CPFFTPTPMVTE----GVDPALIEQLTRAV-PMRRLADPNEVVSAMLHMVNPDNGFMTGQ 237

Query: 259 CITIDGGRSVM 269
            I IDGG S +
Sbjct: 238 AIAIDGGVSAI 248


Lambda     K      H
   0.321    0.138    0.424 

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: 143
Number of extensions: 6
Number of successful extensions: 4
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: 272
Length of database: 248
Length adjustment: 24
Effective length of query: 248
Effective length of database: 224
Effective search space:    55552
Effective search space used:    55552
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 (21.9 bits)
S2: 47 (22.7 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