GapMind for catabolism of small carbon sources

 

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

Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate 5208014 Shew_0530 FAD dependent oxidoreductase (RefSeq)

Query= SwissProt::Q9LES4
         (483 letters)



>FitnessBrowser__PV4:5208014
          Length = 375

 Score =  285 bits (729), Expect = 2e-81
 Identities = 169/408 (41%), Positives = 227/408 (55%), Gaps = 39/408 (9%)

Query: 78  ERVDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSL 137
           +++D +VIGAGVVGLAVA  LS R   VLI+D A + GT  SSRNSEV+HAGIYYP  SL
Sbjct: 2   DKLDAIVIGAGVVGLAVAASLSRRFGNVLIIDRAETIGTGISSRNSEVIHAGIYYPTGSL 61

Query: 138 KAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLE 197
           KA+ CV G+  LY YC    +    +GKLIVAT   +  +LD L      N V  L  L 
Sbjct: 62  KAQLCVEGKRQLYAYCRRRGVAVNSLGKLIVATQVEQEAQLDALFTQARANGVDDLNPLG 121

Query: 198 GFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNH 257
             +   +EP L+    LLSP +GI+D+H  MLSL+ ++ ++            G     H
Sbjct: 122 RRQLQALEPALKASAGLLSPSTGIVDSHGLMLSLLAEAEEY------------GAIFCPH 169

Query: 258 ATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKR 317
             F       NG               F     +   ++ L  + ++N AGL A  +A R
Sbjct: 170 TEFITTQADANG---------------FRVELMQQGERVSLETSFLINCAGLFATEVATR 214

Query: 318 LHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEG--GLGVHVTVDLNGLVKFG 375
           + GL    VP  ++ +G YF   G    PF  L+YP+PE G  GLG+H T+DL G +KFG
Sbjct: 215 IEGLAESLVPQLYWCKGHYFAYQG--KSPFAHLIYPVPEPGLKGLGIHATIDLGGQLKFG 272

Query: 376 PDVEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSG 435
           PD +++    D+       DYRV     ++F+  I  YYP +    L+  Y+GIRPKL G
Sbjct: 273 PDAQYM--VPDSLE-----DYRVPEALRQRFHQAIASYYPGIAIERLQTAYAGIRPKLQG 325

Query: 436 PKQSP-ADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIANKFL 482
           P  +  ADF+IQGE  HG+PGLVNL GIESPGLT+SLAIAE ++ + +
Sbjct: 326 PDDTEVADFLIQGEAQHGIPGLVNLLGIESPGLTASLAIAEQVSRQLV 373


Lambda     K      H
   0.318    0.136    0.401 

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: 505
Number of extensions: 28
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 483
Length of database: 375
Length adjustment: 32
Effective length of query: 451
Effective length of database: 343
Effective search space:   154693
Effective search space used:   154693
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 (21.7 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