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_084199172.1 C0029_RS09065 acyl-CoA dehydrogenase

Query= BRENDA::Q18AQ1
         (378 letters)



>NCBI__GCF_002869505.1:WP_084199172.1
          Length = 378

 Score =  273 bits (699), Expect = 4e-78
 Identities = 150/377 (39%), Positives = 228/377 (60%), Gaps = 3/377 (0%)

Query: 3   LNSKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEG 62
           +++++  + +++     E E++P     +E+   P E    +  AG++    P+ YGG G
Sbjct: 1   MDNEELTLFRDMARRAYEQEIEPHYEGWEEQHLVPRELWNTLGAAGLLCPDMPEAYGGAG 60

Query: 63  GDTVGYIMAVEELSRVCGTTGVI--LSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLG 120
                 +  +EE+SR+ G  G+      H+++ +  I  +G EEQKQ++L  + +GE +G
Sbjct: 61  TSPRVCLAMIEEMSRM-GFGGLASGYGIHSNIVAPYINHFGTEEQKQQWLPKMITGEAVG 119

Query: 121 AFGLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGI 180
           A  +TEP AG+D  G +TTAV DG+E++LNGSKIFITN I  D+ +V A+TD  KG KG 
Sbjct: 120 ALAMTEPGAGSDVQGIRTTAVRDGEEWVLNGSKIFITNGIHADLVIVAAITDPGKGAKGT 179

Query: 181 SAFIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDG 240
           S F+V+   PGF  G K +K+G   S T+EL F+D R+P   LLG+E +GF I M+ L  
Sbjct: 180 SLFLVDASLPGFEKGNKIEKIGQHASDTAELFFQDVRLPASALLGEENKGFVIMMTELPR 239

Query: 241 GRIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQ 300
            R+GIAAQA+  A+GA+D TV YV ER  FG+ ++ FQNT+F LA+++ ++   R L  +
Sbjct: 240 ERLGIAAQAVAAAEGAMDITVDYVLERKAFGQTVASFQNTRFTLAEVKTEIALNRALYEK 299

Query: 301 AAINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEI 360
            A +   G+    +AAM K    E       + +QL GGYGYT +YP+ R   DA+I  I
Sbjct: 300 CADDYARGELTADDAAMLKYANTEMQCSTIDQCLQLFGGYGYTAEYPISRYYTDARIQRI 359

Query: 361 YEGTSEVQRMVISGKLL 377
           Y GTSE+ R +++  +L
Sbjct: 360 YGGTSEIMRELVARSIL 376


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: 390
Number of extensions: 23
Number of successful extensions: 2
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: 378
Length adjustment: 30
Effective length of query: 348
Effective length of database: 348
Effective search space:   121104
Effective search space used:   121104
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