GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Bacillus altitudinis 41KF2b

Align Enoyl-CoA isomerase/hydratase fer4; Fe-regulated protein 4; Ferrichrome A biosynthesis protein fer4; EC 4.2.1.17 (characterized)
to candidate WP_035704417.1 BA79_RS18210 enoyl-CoA hydratase

Query= SwissProt::Q4PEN0
         (274 letters)



>NCBI__GCF_000691145.1:WP_035704417.1
          Length = 260

 Score =  202 bits (513), Expect = 8e-57
 Identities = 109/252 (43%), Positives = 157/252 (62%), Gaps = 8/252 (3%)

Query: 23  LVLDRPEARNAISRSLLQDVLQCLQVLVCKITQPKQDEPLPRVLILRANGPCFCAGADLK 82
           + L+RP   NA+S ++L+++ Q +Q +       K D  +  +L+  A    FCAGADLK
Sbjct: 17  MTLNRPAQANALSAAMLEEINQTIQEI-------KHDANIRCLLMTGAGAKVFCAGADLK 69

Query: 83  ERREMSEAEVIEFLQDLRHMLEQVEKLPIPTLAAIDGPALGGGLELALACDFRIAAETVS 142
           ERR M+E E  E +  ++     +E LP+P +A I+G ALGGGLELALACD RIA    +
Sbjct: 70  ERRLMTEQEAKEAVLTIQQTFTDIESLPVPVIAVINGHALGGGLELALACDLRIARAGAA 129

Query: 143 KIGFPEVKLGIIPGAGGTQRAPRIIGMQRAKELIYTGTQLNATQAKDLGLIDHVAPGSTC 202
            +G PE  L I+PGAGGTQR PR+IG  +AKE+I+TGT L A +A  +GLI+ ++   + 
Sbjct: 130 -LGLPETGLAILPGAGGTQRLPRLIGPGKAKEMIFTGTSLRAEEAVQIGLIERISTADSL 188

Query: 203 LKLCQELAQQMMPSAPLALRAAKMAISMGANVELARGLDLEWACYEPLLESKDRREALDA 262
           +     LA+Q+  + P+AL+ AK AI    + +L  GL  E+  Y  L+ ++DR E L A
Sbjct: 189 MNDAITLAKQITKNGPIALKEAKQAIQSSLDHDLQTGLTKEYEAYLRLIHTEDRLEGLKA 248

Query: 263 FQQKRKPIFTGK 274
           FQ+KR P + GK
Sbjct: 249 FQEKRTPHYRGK 260


Lambda     K      H
   0.320    0.136    0.394 

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: 169
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: 274
Length of database: 260
Length adjustment: 25
Effective length of query: 249
Effective length of database: 235
Effective search space:    58515
Effective search space used:    58515
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 (21.8 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