GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Halioglobus japonicus S1-36

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 WP_084200594.1 C0029_RS01670 acyl-CoA dehydrogenase

Query= BRENDA::D2RL84
         (383 letters)



>NCBI__GCF_002869505.1:WP_084200594.1
          Length = 386

 Score =  287 bits (734), Expect = 4e-82
 Identities = 163/381 (42%), Positives = 229/381 (60%), Gaps = 3/381 (0%)

Query: 1   MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60
           MDF+L EDQ    D A  FAE  LAP     D+  I+ +  + + GE GF G+  PE  G
Sbjct: 1   MDFSLNEDQVAFADSARAFAEGALAPHAARWDEESIFPKDALAQAGELGFMGMYTPESAG 60

Query: 61  GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120
           G+G+  L   L VEEL+K    T   L+ + ++  + I  +        +   +  GT +
Sbjct: 61  GLGMSRLDASLIVEELAKGCTATAAFLTIH-NMATSMIGKYCNASVIDAWCPELVMGTKL 119

Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHG 180
            ++ LTEP AG+DA++ +T+A   GD YI+NG+K+FI+   + D  VV   T    G  G
Sbjct: 120 ASYCLTEPGAGSDAASLRTSAERDGDDYIVNGAKVFISGAGDTDVLVVMLRTG-GPGPKG 178

Query: 181 ISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLD 240
           ISA ++     G  +GK EDKMG +   T  + F++  VP  N LGKEG+GF IAME LD
Sbjct: 179 ISALLIPADAEGISYGKKEDKMGWNAQPTRMVTFDNVRVPVANRLGKEGQGFSIAMEGLD 238

Query: 241 GGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVY 300
           GGRI +A  ++G A+ AL  AV Y +ER+QF  +I++FQA QF +ADM T++ AAR +V 
Sbjct: 239 GGRINIATCSIGTAQQALEEAVAYVQERKQFDTAIAEFQATQFKLADMLTELVAARQMVR 298

Query: 301 HAA-MLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKIT 359
            AA  L N+    S   AMAK FA+DV   V  DA+Q+ GGYGY  +YP ER++R+ ++ 
Sbjct: 299 LAASKLDNKDSQASTYCAMAKRFATDVGFNVCNDALQLHGGYGYIKEYPMERHVRDTRVH 358

Query: 360 QIYEGTNQVMRIVTSRALLRD 380
           QI EGTN++MR++ SR LL D
Sbjct: 359 QILEGTNEIMRVIVSRRLLMD 379


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: 338
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: 383
Length of database: 386
Length adjustment: 30
Effective length of query: 353
Effective length of database: 356
Effective search space:   125668
Effective search space used:   125668
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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