GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__ANA3:7024269 Shewana3_1461 multifunctional
           fatty acid oxidation complex subunit alpha (RefSeq)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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