GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Psychrobacter cryohalolentis K5

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_011513566.1 PCRYO_RS06325 acyl-CoA dehydrogenase

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



>NCBI__GCF_000013905.1:WP_011513566.1
          Length = 384

 Score =  285 bits (728), Expect = 2e-81
 Identities = 151/369 (40%), Positives = 227/369 (61%), Gaps = 2/369 (0%)

Query: 9   QISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYA 68
           QI+D  RQF   +L P         R P + I +M ELG FG+ +PE++GG         
Sbjct: 10  QITDTIRQFVNNQLIPMEHWVAENDRLPDDIINQMRELGLFGLTIPEEYGGLGVTMEEEV 69

Query: 69  MALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQA 128
               E+     A  +++  +N +G   ++  G + QK+++L  LASG ++G+F LTEP +
Sbjct: 70  TLAFELGRTSPAFRSLIGTNNGIGSSGLVIDGTEAQKQKYLPRLASGEIIGSFCLTEPDS 129

Query: 129 GSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRG-ISAFIVPTD 187
           GSDA+SLKT A  +GD Y++NG K++IT+   AGV  V A TDP   + G ISAFIV +D
Sbjct: 130 GSDAASLKTTAIKDGDTYIINGTKRYITNAPEAGVFTVMARTDPQNKRSGGISAFIVESD 189

Query: 188 SPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGE-EGEGYKIALANLEGGRVGIAS 246
           +PG  + +++ K+GQ  + TC ++F++  VP    +G  EG G+K A+  L+ GR+ IA+
Sbjct: 190 TPGITLGKIDKKMGQKGAHTCDVIFDNCIVPADALIGGVEGVGFKTAMKVLDKGRLHIAA 249

Query: 247 QSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDS 306
            S G A    + A  YA ER+ FG+PI   Q +   LAD   +I  A+ MV  A+ LRD 
Sbjct: 250 ASTGAATRMLDDALHYAVERKQFGQPIANFQLIQAMLADSKAEIYAAKSMVLDASRLRDE 309

Query: 307 GKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDI 366
           GK  + E+S AK+FA+EM  +V   A+Q  GG GY++D+ +ER YRDVR+ ++YEGT+ I
Sbjct: 310 GKDVVTESSCAKMFATEMCGRVADRAVQIHGGAGYIADYGIERFYRDVRLYRLYEGTTQI 369

Query: 367 QRMVISRNL 375
           Q+++I+RN+
Sbjct: 370 QQIIIARNM 378


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: 323
Number of extensions: 12
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: 375
Length of database: 384
Length adjustment: 30
Effective length of query: 345
Effective length of database: 354
Effective search space:   122130
Effective search space used:   122130
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