GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Erythrobacter marinus HWDM-33

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_047094365.1 AAV99_RS12275 enoyl-CoA hydratase/isomerase family protein

Query= reanno::psRCH2:GFF2389
         (257 letters)



>NCBI__GCF_001013305.1:WP_047094365.1
          Length = 252

 Score =  103 bits (258), Expect = 3e-27
 Identities = 85/259 (32%), Positives = 121/259 (46%), Gaps = 21/259 (8%)

Query: 6   LLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKA--FAA 63
           L ++    VA + ++R    NA N  +   +   L Q  ADP +  +V+  +     F A
Sbjct: 3   LRLEFDGPVAHLLIDRLDKRNAFNMAMWEAMPGLLEQARADPAVRTLVIRSAQPGGVFCA 62

Query: 64  GADIKEM-------AELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLC 116
           GADIKEM       A L   Q  ++    D  R+     P +A V G  +GGGC +A+ C
Sbjct: 63  GADIKEMLLHKDDGAWLAANQAAINRVQHDLARLTL---PTVAFVEGDCVGGGCGIAIAC 119

Query: 117 DMIFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLV 176
           D+  A D ARFG     LG++  +   + LT  VG  +A  M  TG  +DAAEA+R GLV
Sbjct: 120 DLRVATDKARFGITPGKLGIVYPLHDVKLLTDLVGPGQAKRMLFTGGLLDAAEAQRIGLV 179

Query: 177 ARVFPA-ESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFA 235
             +  +   LL + L A       S  +   IK  V R  +    +  +    +F   F 
Sbjct: 180 EMIADSPRGLLNDILSA-------SPHSIREIKMFVRRVLDGQTGDDDQ-TLAIFTDAFM 231

Query: 236 TADQKEGMAAFSEKRKPEF 254
             D  EG AAF+ KRKP+F
Sbjct: 232 RGDFAEGAAAFAGKRKPDF 250


Lambda     K      H
   0.321    0.135    0.375 

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: 130
Number of extensions: 7
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: 257
Length of database: 252
Length adjustment: 24
Effective length of query: 233
Effective length of database: 228
Effective search space:    53124
Effective search space used:    53124
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 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