GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Shewanella sp. ANA-3

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate 7024269 Shewana3_1461 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= CharProtDB::CH_091794
         (261 letters)



>FitnessBrowser__ANA3:7024269
          Length = 709

 Score =  135 bits (341), Expect = 2e-36
 Identities = 80/220 (36%), Positives = 129/220 (58%), Gaps = 7/220 (3%)

Query: 1   MELNNVILEKEGKVAVVTINRP-KALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGE 59
           ME    +  +E  +A++ ++ P + +N L ++   E+  ++ EI+ DS +  ++L    +
Sbjct: 1   MEKTFNLTRREDGIAILMMDVPGETMNTLKAEFGPEISEILSEIKRDSSIRGLVLISGKK 60

Query: 60  KSFVAGADISEMKEMNTI-EGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMS 118
            SFVAGADIS +    T  + +     G+ VF  LE L  PV+AA++G  LGGG E+A++
Sbjct: 61  DSFVAGADISMLDACQTAGDAKALSQQGHVVFNELEALNIPVVAAIHGACLGGGLELALA 120

Query: 119 CDIRIASSNAR--FGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRI 176
           C  R+ S + +   G PEV LG+ PG GGTQRL RLVG+  A  ++ T + I+  +AL++
Sbjct: 121 CHQRVCSDDGKTMLGVPEVQLGLLPGGGGTQRLPRLVGITTALDMMLTGKQIRPKQALKM 180

Query: 177 GLVNKVVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINR 216
           GLVN VV  + L+ TA E+A   ++    A  + K  +N+
Sbjct: 181 GLVNDVVPQTILLQTAVEMA---LAGKRTAKPVKKSLVNQ 217


Lambda     K      H
   0.317    0.134    0.365 

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: 408
Number of extensions: 22
Number of successful extensions: 3
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: 261
Length of database: 709
Length adjustment: 32
Effective length of query: 229
Effective length of database: 677
Effective search space:   155033
Effective search space used:   155033
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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