GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Halomonas xinjiangensis TRM 0175

Align Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial; HCDH; Medium and short-chain L-3-hydroxyacyl-coenzyme A dehydrogenase; Short-chain 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_081948961.1 JH15_RS09265 hypothetical protein

Query= SwissProt::P00348
         (314 letters)



>NCBI__GCF_000759345.1:WP_081948961.1
          Length = 461

 Score =  229 bits (583), Expect = 1e-64
 Identities = 120/287 (41%), Positives = 174/287 (60%), Gaps = 6/287 (2%)

Query: 27  VKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENP 86
           + H+ VIG G+MG GIAQ++A  G    L D      A +++ + E+L     K+  +  
Sbjct: 5   IDHIAVIGAGIMGQGIAQISAQQGVITTLYDVQPGAAAAARERVAEAL-----KRRIDKG 59

Query: 87  KAGDEFVEKTLSSISTSTDAASVVHSTDLVVEAIVENLKVKSELFKRLDKFAAEHTIFAS 146
           +  D   ++TLS +  + +    +   DLVVEAIVE+L VK +LF+RL+     H +  S
Sbjct: 60  RMSDAEAQETLSRVRLA-ETFEALGDADLVVEAIVEDLAVKRDLFRRLEAICGAHALLCS 118

Query: 147 NTSSLQITSLANATTRQDRFAGLHFFNPVPLMKLVEVVKTPMTSQKTLESLVDFSKTLGK 206
           NTSSL I ++A   T   R AGLHFFNP P M+LVEVV  P TS+ T ++L++F++TLGK
Sbjct: 119 NTSSLSIGAIAEGLTAPQRVAGLHFFNPAPAMRLVEVVSAPDTSEATRDALLEFARTLGK 178

Query: 207 HPVSCKDTPGFIVNRLLVPYLIEAVRLYERGDASKEDIDTAMKLGAGYPMGPFELLDYVG 266
            PV+  D+PGFIVNR   P+  EA+ L E+G A  E +D  +  G G+P+GPF L+D VG
Sbjct: 179 TPVAVNDSPGFIVNRCARPFYGEALHLLEQGTADAETLDACLTCGGGFPLGPFALIDLVG 238

Query: 267 LDTTKFIIDGWHEMDSQNPLFQPSPAMNKLVAENKFGKKTGEGFYKY 313
           +D          E   ++P F+PSP +   VA  + GKK+G+GFY++
Sbjct: 239 VDINLKATTTLWEAFGRHPRFRPSPLIEAKVAAGELGKKSGQGFYRH 285



 Score = 52.4 bits (124), Expect = 2e-11
 Identities = 26/80 (32%), Positives = 46/80 (57%)

Query: 197 LVDFSKTLGKHPVSCKDTPGFIVNRLLVPYLIEAVRLYERGDASKEDIDTAMKLGAGYPM 256
           L++ + TLG   V   D PG +V R+    + EA R    G A+ + +DTAM+LG  + +
Sbjct: 370 LIEAAATLGVRLVEVPDRPGLVVLRVATMLIGEARRALAEGVATADAMDTAMRLGLNFAL 429

Query: 257 GPFELLDYVGLDTTKFIIDG 276
           GP+++L+ +G +  +  + G
Sbjct: 430 GPWDMLERLGSEPVETTLAG 449


Lambda     K      H
   0.315    0.130    0.359 

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: 316
Number of extensions: 8
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 314
Length of database: 461
Length adjustment: 30
Effective length of query: 284
Effective length of database: 431
Effective search space:   122404
Effective search space used:   122404
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 (21.6 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