GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Marinobacter adhaerens HP15

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized)
to candidate GFF928 HP15_907 acyl-CoA dehydrogenase domain protein

Query= BRENDA::D2RL84
         (383 letters)



>FitnessBrowser__Marino:GFF928
          Length = 388

 Score =  300 bits (768), Expect = 5e-86
 Identities = 161/382 (42%), Positives = 233/382 (60%), Gaps = 3/382 (0%)

Query: 1   MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60
           MDFNLTEDQ   ++ A  FAEK +AP   + D  HI+   ++ + GE GF G+  PE  G
Sbjct: 1   MDFNLTEDQLAFREAARAFAEKSMAPHAAKWDNEHIFPVDMMKEAGEMGFMGMYTPEALG 60

Query: 61  GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120
           GMGL  L   + VEEL+     T   ++ + ++    +  F +++ KQ+ +  +A G  +
Sbjct: 61  GMGLSRLDTSVIVEELAAACPSTAAFITIH-NMATWMVASFASDDLKQEIVPKLASGEWL 119

Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDK-SQGVH 179
            ++ LTEP AG+DA++ +T AV  GD Y++NGSK+FI+     D  V+ A T     G  
Sbjct: 120 ASYCLTEPGAGSDAASLRTKAVRDGDSYVINGSKVFISGAGATDILVLMARTGAPDSGYK 179

Query: 180 GISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETL 239
           GIS F++     G  +GK E+KMG H+  T  +  E+  +P  N +G EG+GF IAM+ L
Sbjct: 180 GISTFVIPADADGISYGKNEEKMGWHSQPTRMISLENVRIPASNRVGDEGDGFAIAMKGL 239

Query: 240 DGGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLV 299
           DGGR+ +A  +LG A+ AL  A  Y  EREQFG+ ++ FQALQF +ADMAT + AAR +V
Sbjct: 240 DGGRLNIATCSLGGAQAALLRARNYMHEREQFGKPLAAFQALQFKLADMATNLVAARQMV 299

Query: 300 YHAAMLKNEGKPYSEA-AAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKI 358
              A   +   P +    AMAK FA+D   EV  +A+Q+ GGYGY  +YP ERY+R+ ++
Sbjct: 300 RLGAFKLDNADPEATLHCAMAKRFATDACFEVVNEALQLHGGYGYIREYPLERYLRDLRV 359

Query: 359 TQIYEGTNQVMRIVTSRALLRD 380
            QI EGTN++MR++ +R LL D
Sbjct: 360 HQILEGTNEIMRLIVARRLLDD 381


Lambda     K      H
   0.318    0.134    0.379 

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: 346
Number of extensions: 13
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: 383
Length of database: 388
Length adjustment: 30
Effective length of query: 353
Effective length of database: 358
Effective search space:   126374
Effective search space used:   126374
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