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 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_084198396.1 C0029_RS13540 acyl-CoA dehydrogenase

Query= BRENDA::Q18AQ1
         (378 letters)



>NCBI__GCF_002869505.1:WP_084198396.1
          Length = 385

 Score =  247 bits (630), Expect = 4e-70
 Identities = 136/376 (36%), Positives = 217/376 (57%), Gaps = 4/376 (1%)

Query: 5   SKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGD 64
           +++ +ML +  + F E E+ P     + +     +       AG++    P EYGG GGD
Sbjct: 10  NEELRMLHDSALKFTEQELGPNRERWEAQGMCDRDAWRTTGAAGLLCASIPVEYGGAGGD 69

Query: 65  TVGYIMAVEELSR--VCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAF 122
                +  + + R     + G   + H+ + +  I  YG E+QK K+L  +A+GE +GA 
Sbjct: 70  YTHEAVIYDAMIRGGAAASVGGGNTVHSQIVAHYILDYGTEDQKHKWLPAMAAGELVGAI 129

Query: 123 GLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISA 182
            +TEP AG+D  G +TTAV +GDEYI+NG+K FI+N    ++ +V+A TD + G KG S 
Sbjct: 130 AMTEPGAGSDLQGVKTTAVREGDEYIINGAKTFISNGQHAELIIVVAKTDPAAGAKGTSL 189

Query: 183 FIVE-KGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGK-EGQGFKIAMSTLDG 240
            +VE +G  GF+ G    K+G++ + TSEL F + R+P  NLLG  EGQGF   M  L  
Sbjct: 190 IVVETEGLDGFARGRNLDKVGLKDADTSELFFNNVRVPTANLLGDPEGQGFIQLMMQLPQ 249

Query: 241 GRIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQ 300
            R+GIA     +A+ A++ T++Y ++R  FG+ +  FQNT+F+LA+ + +   AR  V Q
Sbjct: 250 ERLGIACAGATIAEMAVETTLEYTRDRAAFGKSVFDFQNTRFKLAECKTEATIARSFVDQ 309

Query: 301 AAINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEI 360
                  G+    EA+MAK +  +   ++  + +QLHGGYGY  +YP+ RM  D+++ +I
Sbjct: 310 CIAKHINGELSAEEASMAKWWCTQKQCDIVDECLQLHGGYGYMWEYPIARMYADSRVQKI 369

Query: 361 YEGTSEVQRMVISGKL 376
           Y GT+E+ + +I+  L
Sbjct: 370 YGGTNEIMKELIARSL 385


Lambda     K      H
   0.315    0.133    0.373 

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: 15
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: 378
Length of database: 385
Length adjustment: 30
Effective length of query: 348
Effective length of database: 355
Effective search space:   123540
Effective search space used:   123540
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: 42 (22.0 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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