GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Algoriphagus aquaeductus T4

Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_111393848.1 CLV31_RS15640 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-11693
         (386 letters)



>NCBI__GCF_003253485.1:WP_111393848.1
          Length = 401

 Score =  219 bits (558), Expect = 1e-61
 Identities = 133/383 (34%), Positives = 210/383 (54%), Gaps = 12/383 (3%)

Query: 1   MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60
           +D  LT E + +R ++ +F    ++P I D+ ++  FPYEIV++ G +G FG   P EYG
Sbjct: 23  LDDLLTEEQKLIRSSIRDFVKKEISPYIEDWAQKAHFPYEIVKKFGEVGAFGPQLPVEYG 82

Query: 61  GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEIL 120
             G DY++ G+ ++E+ R DS +  T     SL   PI+ FGT+ Q+ ++LPRL SGE+L
Sbjct: 83  CGGLDYISYGLIMQEIERGDSGMRSTASVQGSLVMYPIYKFGTEEQRLKYLPRLASGELL 142

Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180
           G FGLTEPD GS+     T  +  +  + +++NG K +I+NS         +  V  +  
Sbjct: 143 GCFGLTEPDHGSNPSGMVTNFK--DMGDHYLLNGAKMWISNSPK-----ADIAVVWAKNE 195

Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLL-GEQGRGYAQ 239
           +G+  I  +IV  G  GF+    ++K    AS T EL F +V+VP  NLL G+ G G   
Sbjct: 196 EGR--IQGLIVERGMEGFSTPETHNKWSLRASCTGELVFDNVKVPKENLLPGKTGLGAP- 252

Query: 240 FLRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHM 299
            +  LD  R  I+  A G A  C + + +YA ER  FG+ IG +Q  Q K+A+M  +   
Sbjct: 253 -MMCLDSARFGIAWGAIGAAMDCYESARRYAAERIQFGKPIGGFQLTQKKLAEMLTEITK 311

Query: 300 ARVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWR 359
           A++        +  G+      ++AK  +  +A++ AREA QIHGG G   EYP+ R   
Sbjct: 312 AQLLAWKVGKMMNEGKAKTVHISMAKRNNVEMALNIAREARQIHGGMGITGEYPIMRHMM 371

Query: 360 DSKILEIGEGTSEVQRMLIAREL 382
           + + +   EGT ++  +++  E+
Sbjct: 372 NLESVITYEGTHDIHLLILGNEI 394


Lambda     K      H
   0.318    0.136    0.402 

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: 411
Number of extensions: 19
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: 386
Length of database: 401
Length adjustment: 31
Effective length of query: 355
Effective length of database: 370
Effective search space:   131350
Effective search space used:   131350
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.

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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