GapMind for catabolism of small carbon sources

 

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

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 7025788 Shewana3_2938 iron-containing alcohol dehydrogenase (RefSeq)

Query= BRENDA::A4IP64
         (395 letters)



>FitnessBrowser__ANA3:7025788
          Length = 382

 Score =  229 bits (585), Expect = 8e-65
 Identities = 132/359 (36%), Positives = 208/359 (57%), Gaps = 5/359 (1%)

Query: 4   ARIVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVH 63
           A+   P ++ +G GA++  + ++K LG K  L++TD  LVKIGLV +V   L Q G +  
Sbjct: 3   AKFFIPSVNVLGKGAVNDAIGDIKTLGFKRALIVTDKPLVKIGLVGEVAEKLGQNGITST 62

Query: 64  VYTDVVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNL 123
           V+  V P P +   E  +A  +  + D VI +GGGS  D AK  A++A + GS+ DY  L
Sbjct: 63  VFDGVQPNPTVGNVEAGLALLKANQCDFVISLGGGSPHDCAKGIALVATNGGSIKDYEGL 122

Query: 124 TGTRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDPQLT 181
             +    K  LP + I TT+GT SE+T   +++ E    K  +   +    +++ DP+L 
Sbjct: 123 DQSA---KPQLPLVAINTTAGTASEMTRFCIITDEARHIKMAIVDKHTTPLLSVNDPELM 179

Query: 182 VSVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQAR 241
           +  P  +TAATG+DALTHAVEAYVS+ A+P +D  A+ AI LI  +L  AV  G D +AR
Sbjct: 180 LKKPASLTAATGMDALTHAVEAYVSIAANPITDACAIKAIELIQGNLVNAVKQGQDIEAR 239

Query: 242 IDMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRM 301
             MA   +LAG+AF NA +  VHA+A+ LGG + + HG  NA+LLP+V  Y  +   +R+
Sbjct: 240 EQMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYDLPHGVCNALLLPHVQEYNAKVVPERL 299

Query: 302 ADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQ 360
            DI  A+G + + +++ + +   +  ++     V IP+ L   G+    + +L ++A++
Sbjct: 300 KDIAKAMGVDVANMTDEQGAAAAIAAIKALSVAVNIPENLTLLGVKAEDIPTLAENALK 358


Lambda     K      H
   0.318    0.135    0.381 

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: 344
Number of extensions: 14
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: 395
Length of database: 382
Length adjustment: 30
Effective length of query: 365
Effective length of database: 352
Effective search space:   128480
Effective search space used:   128480
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: 50 (23.9 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