GapMind for catabolism of small carbon sources

 

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

Align 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; EC 1.2.4.4 (characterized)
to candidate 7024960 Shewana3_2131 dehydrogenase, E1 component (RefSeq)

Query= SwissProt::O45924
         (431 letters)



>FitnessBrowser__ANA3:7024960
          Length = 392

 Score =  368 bits (944), Expect = e-106
 Identities = 187/365 (51%), Positives = 240/365 (65%), Gaps = 3/365 (0%)

Query: 59  LPIYRVTNAVGDVIDKSQDPNFDEQTSLKMYKTMTQLNIMDRILYDSQRQGRISFYMTSF 118
           +PI R+  A G   + +  P  DE  + K+Y T     ++D  +  +QRQGRISFYMT  
Sbjct: 24  IPILRILQADGTTYETAVLPVIDEALATKIYDTCVFTRVLDERMLGAQRQGRISFYMTCT 83

Query: 119 GEEGNHVGSAAALEPQDLIYGQYREAGVLLWRGYTMENFMNQCYGNADDLGKGRQMPMHF 178
           GEE   VGS AAL+ +D+I  QYRE   L +RG+T E FMNQ + N  DLGKGRQMP+H+
Sbjct: 84  GEEAAIVGSVAALDQEDVILAQYREHAALRYRGFTTEQFMNQMFSNEKDLGKGRQMPIHY 143

Query: 179 GTKERNFVTISSPLTTQLPQAVGSAYAFKQQKDNNRIAVVYFGDGAASEGDAHAAFNFAA 238
           G    N+ TISSPL TQ+PQA G  Y+ K Q   N +AV YFG+GAASEGD HA  N AA
Sbjct: 144 GCAALNYQTISSPLATQIPQATGVGYSLKMQGKRN-VAVCYFGEGAASEGDFHAGLNMAA 202

Query: 239 TLKCPIIFFCRNNGYAISTPTSEQYGGDGIAGKGPAYGLHTIRVDGNDLLAVYNATKEAR 298
            LKCP+IFFCRNNGYAISTPT EQ+ G+GIA +G  YG+HTIRVDGND+LAV  AT++AR
Sbjct: 203 VLKCPVIFFCRNNGYAISTPTEEQFAGNGIASRGVGYGMHTIRVDGNDMLAVLAATQQAR 262

Query: 299 RVALT-NRPVLIEAMTYRLGHHSTSDDSTAYRSSDEVQTWGDKDHPITRFKKYITERGWW 357
             A+  N PVLIEAMTYRLG HS+SDD + YRS +E   W   D P+ RFK ++  +GW 
Sbjct: 263 AYAIEHNAPVLIEAMTYRLGAHSSSDDPSGYRSKEEEAKWQQHD-PVKRFKLWLINKGWL 321

Query: 358 NEEKEMEWQKEVKKRVLTEFAAAEKRKKAHYHDLFEDVYDELPLRLRRQRDELDAHVAEY 417
            E  + +  ++ ++ VL     AEK       ++ EDVYD+    L++Q  EL  H+ +Y
Sbjct: 322 AEADDAQRYEKYREEVLAAVKVAEKLPIPMLDEIIEDVYDKPTPALKKQLSELKEHIKKY 381

Query: 418 KEHYP 422
            + YP
Sbjct: 382 PQSYP 386


Lambda     K      H
   0.317    0.132    0.391 

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: 477
Number of extensions: 20
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: 431
Length of database: 392
Length adjustment: 31
Effective length of query: 400
Effective length of database: 361
Effective search space:   144400
Effective search space used:   144400
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