GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Shewanella sp. ANA-3

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 7025944 Shewana3_3092 succinate semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__ANA3:7025944
          Length = 482

 Score =  329 bits (844), Expect = 1e-94
 Identities = 176/467 (37%), Positives = 272/467 (58%), Gaps = 3/467 (0%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPD-GQAEDARKAIDAAERAQPEWEALPAIER 68
           YI+GQ+   +    + + NPAT AVI+ +P  GQAE  + AI AAE A P W AL A ER
Sbjct: 14  YINGQWCDAQSKETVAIANPATGAVIASVPVMGQAE-TQAAIAAAEAALPAWRALTAKER 72

Query: 69  ASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128
              LR+    + E + +++ ++  E GK    A+ EV + A +I++ AE A+R  G+ I 
Sbjct: 73  GVKLRRWFELLNENSDDLALMMTSEQGKPLAEAKGEVTYAASFIEWFAEEAKRVYGDTIP 132

Query: 129 SDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAF 188
             +  + I++ K+ +GVT  I PWNFP  +I RK APAL  G T+V+KP+  TP  A+A 
Sbjct: 133 GHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPFTALAL 192

Query: 189 AKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248
           A + +  G+P GVF+++ G    +G E+  NP V  +S TGS   G K+M   A  + K+
Sbjct: 193 AVLAERAGIPAGVFSVITGDAIGIGNEMCSNPVVRKLSFTGSTQVGIKLMEQCAPTLKKL 252

Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308
            LELGG AP IV DDA+++ AV+  + ++  N+GQ C CA R+YVQ G+YD+F  +L  A
Sbjct: 253 SLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFARKLSIA 312

Query: 309 MQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPT 368
           +  ++ G       +  GPLIN AA+E+V+  +  A+ +GA V  GGK     G ++ PT
Sbjct: 313 VGKLKVGEGIGEG-VTTGPLINCAAVEKVQSHLEDALSKGATVVAGGKPHSLGGNFFEPT 371

Query: 369 LLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIK 428
           +L +V   M +  EETFGP+ P+  F  ++D I  AND+++GL +  Y +++++  K  +
Sbjct: 372 VLTNVDSSMRVAREETFGPLAPLFKFTDVDDVIKQANDTEFGLAAYFYGRDISLVWKVTE 431

Query: 429 GLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475
            L++G   +N            G + SG+G    K G+ EYL+ + +
Sbjct: 432 ALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKFGIEEYLEIKYI 478


Lambda     K      H
   0.318    0.135    0.392 

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: 556
Number of extensions: 28
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: 479
Length of database: 482
Length adjustment: 34
Effective length of query: 445
Effective length of database: 448
Effective search space:   199360
Effective search space used:   199360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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