GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Pseudomonas fluorescens FW300-N2E3

Align Methylglutaconyl-CoA hydratase, mitochondrial; AU-specific RNA-binding enoyl-CoA hydratase; AU-binding enoyl-CoA hydratase; muAUH; Itaconyl-CoA hydratase; EC 4.2.1.18; EC 4.2.1.56 (characterized)
to candidate AO353_25675 AO353_25675 enoyl-CoA hydratase

Query= SwissProt::Q9JLZ3
         (314 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25675
          Length = 257

 Score =  150 bits (379), Expect = 3e-41
 Identities = 90/258 (34%), Positives = 152/258 (58%), Gaps = 8/258 (3%)

Query: 57  LEEENRGIVVLGINRAYGKNALSKNLLKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAGA 116
           LE + R + ++ +NR    NAL+  ++  L+ A+D L+++ ++  I++       F AGA
Sbjct: 8   LEVQGR-VGLITLNRPQALNALNAQIVSELNHALDGLEANPEIGCIVLTGSKKA-FVAGA 65

Query: 117 DLKERAKMHSSEVGPFVSKIRSVINDIANLPVPTIAAIDGLALGGGLELALACDIRVAAS 176
           D+KE A++   ++  ++  + S  + +AN   P IAA+ G ALGGG ELAL CD  +A  
Sbjct: 66  DIKEMAELTYPQI--YLDDLFSDSDRVANRRKPVIAAVAGFALGGGCELALMCDFILAGD 123

Query: 177 SAKMGLVETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLEQN 236
           +AK G  E  L ++PG GGTQRL RA+G + A E+  S R++D  EA+  G+++ ++  +
Sbjct: 124 NAKFGQPEINLGVLPGMGGTQRLTRAVGKAKAMEMCLSGRLIDAVEAERCGIVARIVPVD 183

Query: 237 QEGDAAYRKALDLAREFLPQGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTISTKDR 296
           +  D A + A  +A++ L   P+AM V K ++N+  EV L  G+  E   +    +T+D+
Sbjct: 184 ELLDEALKVAALIAKKSL---PIAMMV-KESVNRAFEVSLSEGVRFERRVFHAAFATQDQ 239

Query: 297 LEGLLAFKEKRPPRYKGE 314
            EG+ AF  KR  ++ G+
Sbjct: 240 KEGMAAFIAKREAQFVGK 257


Lambda     K      H
   0.318    0.135    0.377 

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: 142
Number of extensions: 9
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: 314
Length of database: 257
Length adjustment: 26
Effective length of query: 288
Effective length of database: 231
Effective search space:    66528
Effective search space used:    66528
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 (21.7 bits)
S2: 47 (22.7 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