GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Porphyrobacter dokdonensis DSW-74

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_068863803.1 I603_RS07850 enoyl-CoA hydratase

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



>NCBI__GCF_001677335.1:WP_068863803.1
          Length = 264

 Score =  267 bits (682), Expect = 2e-76
 Identities = 144/264 (54%), Positives = 184/264 (69%), Gaps = 7/264 (2%)

Query: 1   MTFETLLVDIQER----VALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTG 56
           MT+ET+  +        V L+T+NRPQALNALN +++ EL  A    +AD    C +LTG
Sbjct: 1   MTYETITAETDAHGTKGVTLLTINRPQALNALNSKVLEELIDAFAAYQADATQLCAILTG 60

Query: 57  SA-KAFAAGADIKEMAELTYPQIYLDDFFAD--ADRIATRRKPLIAAVAGYALGGGCELA 113
           S  KAFAAGADIKEM+E      YLDDFF+   ++ +   RKP IAAV G+ALGGGCELA
Sbjct: 61  SGDKAFAAGADIKEMSEKPAADFYLDDFFSPWTSEIVKKTRKPWIAAVNGFALGGGCELA 120

Query: 114 LLCDMIFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERA 173
           ++ D I A+D A+FGQPE+ LGV PG+GG+QRLTRA+GK+K+M+MCLTGR M A EAER+
Sbjct: 121 MMADFIIASDKAKFGQPEIKLGVAPGMGGSQRLTRAIGKSKSMEMCLTGRMMGAEEAERS 180

Query: 174 GLVARVFPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAV 233
            LVARV P + L+ ETLK A  IA     AT+  KE VN AFE TL +G+  ERR+F  +
Sbjct: 181 NLVARVVPHDELIAETLKTAATIAAMPPMATIANKEMVNSAFEMTLDQGLIVERRIFQIL 240

Query: 234 FATADQKEGMAAFSEKRKPEFTNR 257
            A+ D+ EGMAAF EKR+ ++  R
Sbjct: 241 TASEDKAEGMAAFIEKREGQWKGR 264


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: 197
Number of extensions: 8
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: 264
Length adjustment: 25
Effective length of query: 232
Effective length of database: 239
Effective search space:    55448
Effective search space used:    55448
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