GapMind for catabolism of small carbon sources

 

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

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__PV4:5210745
          Length = 485

 Score =  315 bits (806), Expect = 3e-90
 Identities = 171/469 (36%), Positives = 276/469 (58%), Gaps = 4/469 (0%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           YIDG++    G+   DVVNPA++ VI+++ D   +D ++AI AA+RA PEW    A ERA
Sbjct: 15  YIDGRWTV--GEQRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPEWSKRSANERA 72

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129
           + +RK    + E   ++  L+  E GK    A+ E+A+ A +ID+ AE  +R  G+ I +
Sbjct: 73  ALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEEGKRVYGDTIPA 132

Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189
               + IL+ K+ +GV   I PWNFP  +IARK A AL  G T V +PS  TP +A+A A
Sbjct: 133 PANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTPLSALAMA 192

Query: 190 KIVDEIGLPRGVFNLVLGRGET-VGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248
           ++ +  G+P GVFN+V+G     +G+ L  +P VA  + TGS + G+ ++A  A ++ KV
Sbjct: 193 ELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQCATSVKKV 252

Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308
            +ELGG AP IV DDAD++ AV+  + S+  N+GQ C C  R++VQKG+   F  +   A
Sbjct: 253 SMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAAAFTEKFTAA 312

Query: 309 MQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPT 368
           +  ++ G+    + + +GP+I+  A++ V + V   V  GA++  GG+  E    +  P 
Sbjct: 313 VANLKLGD-GLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPSELGESFLAPV 371

Query: 369 LLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIK 428
           ++ DV  EM +   E FGPV P+++FD+  +A++MAND++YGL +  Y +++    +  +
Sbjct: 372 IVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDIGRIFRVAE 431

Query: 429 GLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477
           GL++G   +N            G ++SG G    K+GL +YL+ + + L
Sbjct: 432 GLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIKYLCL 480


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: 547
Number of extensions: 24
Number of successful extensions: 3
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: 485
Length adjustment: 34
Effective length of query: 445
Effective length of database: 451
Effective search space:   200695
Effective search space used:   200695
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: 52 (24.6 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