GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ech in Pseudomonas stutzeri RCH2

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF3051 Psest_3109 Enoyl-CoA hydratase/carnithine racemase

Query= BRENDA::Q9I5I4
         (272 letters)



>lcl|FitnessBrowser__psRCH2:GFF3051 Psest_3109 Enoyl-CoA
           hydratase/carnithine racemase
          Length = 272

 Score =  461 bits (1186), Expect = e-135
 Identities = 221/271 (81%), Positives = 251/271 (92%)

Query: 1   MNTAVEPYKASSFDLTHKLTVEKHGHTALITINHPPANTWDRDSLIGLRQLIEHLNRDDD 60
           M+TAVEPY++  FDLTHKLTVEKHGHTALITINHPPANTWDR+SLIGL+Q++EHLN DDD
Sbjct: 1   MSTAVEPYQSGVFDLTHKLTVEKHGHTALITINHPPANTWDRESLIGLKQVVEHLNHDDD 60

Query: 61  IYALVVTGQGPKFFSAGADLNMFADGDKARAREMARRFGEAFEALRDFRGVSIAAINGYA 120
           IYALV++GQG KFFSAGADL +FADGD+ RAREMARRFGEAFEALRDFRGVSIAAING+A
Sbjct: 61  IYALVISGQGEKFFSAGADLKLFADGDRNRAREMARRFGEAFEALRDFRGVSIAAINGFA 120

Query: 121 MGGGLECALACDIRIAERQAQMALPEAAVGLLPCAGGTQALPWLVGEGWAKRMILCNERV 180
           +GGGLECALACD+RIAE+QAQM LPEA+VGLLPCAGGTQAL WLVGEGWAKRMILC ER+
Sbjct: 121 LGGGLECALACDLRIAEQQAQMGLPEASVGLLPCAGGTQALAWLVGEGWAKRMILCGERI 180

Query: 181 DAETALRIGLVEQVVDSGEARGAALLLAAKVARQSPVAIRTIKPLIQGARERAPNTWLPE 240
            AETALRIGL+EQVV+ G+ARG ALLLAA++ARQSPVA+R IKPLI GAR+R P+T+   
Sbjct: 181 TAETALRIGLIEQVVEPGQARGHALLLAARIARQSPVAVRAIKPLIDGARQRLPHTFGAA 240

Query: 241 ERERFVDLFDAQDTREGVNAFLEKRDPKWRN 271
           ERE FV+LF+A+DT EGVNAFLEKRDP+WRN
Sbjct: 241 EREAFVELFEAEDTLEGVNAFLEKRDPRWRN 271


Lambda     K      H
   0.321    0.136    0.412 

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: 340
Number of extensions: 5
Number of successful extensions: 1
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: 272
Length of database: 272
Length adjustment: 25
Effective length of query: 247
Effective length of database: 247
Effective search space:    61009
Effective search space used:    61009
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 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