GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Algoriphagus aquaeductus T4

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_111393797.1 CLV31_RS14820 acyl-CoA dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_25680
         (375 letters)



>NCBI__GCF_003253485.1:WP_111393797.1
          Length = 379

 Score =  368 bits (945), Expect = e-106
 Identities = 183/372 (49%), Positives = 263/372 (70%)

Query: 4   TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63
           T+E L + +AAR+FAQ  L P   + D E +FP E I +M +LGF GM+V  ++ G    
Sbjct: 6   TEEHLAVQEAAREFAQSELLPGVIDRDSEAKFPHEQIKKMGDLGFLGMMVDPKYNGGGMD 65

Query: 64  YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123
            ++Y +A+EE++  D + S  MSV+NS+ C  + K+G+++QK+++L  LA+G +LGAF L
Sbjct: 66  TISYVIAMEELSKIDASASVSMSVNNSLVCWGLEKYGSEEQKQKYLTRLATGEILGAFCL 125

Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183
           +EP+AGSDA+S +T A  NGDHYVLNG K +IT+G  A V +V A TD S G +GIS F+
Sbjct: 126 SEPEAGSDATSQRTSAEWNGDHYVLNGTKNWITNGSTASVYLVIAQTDASKGHKGISVFL 185

Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243
           V     G+ + + EDKLG   SDT  ++F DV+VP  NR+GEEG G+  A+  L GGR+G
Sbjct: 186 VEKGWEGFVIGKKEDKLGIRGSDTHSLMFTDVKVPAENRIGEEGFGFTFAMETLNGGRIG 245

Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303
           IA+Q++G+A  A+E A  Y++ER++FGKPI +HQA+ F+LADMATQI  AR +V+ AA L
Sbjct: 246 IAAQALGIASGAYELALAYSKERKAFGKPISQHQAIQFKLADMATQIEAARLLVYKAAWL 305

Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363
           +D G+     ++MAKL+ASE+A  V   A+Q  GGYGY+ ++ +ER+ RD ++ QIYEGT
Sbjct: 306 KDQGEDYAHASAMAKLYASEVAMNVTVEAVQVHGGYGYVKEYHVERLMRDAKITQIYEGT 365

Query: 364 SDIQRMVISRNL 375
           S+IQR+VISR +
Sbjct: 366 SEIQRIVISRGI 377


Lambda     K      H
   0.319    0.134    0.389 

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: 337
Number of extensions: 11
Number of successful extensions: 1
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: 375
Length of database: 379
Length adjustment: 30
Effective length of query: 345
Effective length of database: 349
Effective search space:   120405
Effective search space used:   120405
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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