GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Herbaspirillum seropedicae SmR1

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate HSERO_RS12745 HSERO_RS12745 enoyl-CoA hydratase

Query= CharProtDB::CH_091794
         (261 letters)



>FitnessBrowser__HerbieS:HSERO_RS12745
          Length = 260

 Score =  167 bits (424), Expect = 2e-46
 Identities = 93/249 (37%), Positives = 138/249 (55%), Gaps = 1/249 (0%)

Query: 5   NVILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVA 64
           N+ LEK G  AV+T++ P A N      L ++  ++ E+  D ++  +++TG GEK F A
Sbjct: 6   NLKLEKTGHTAVLTLSNPPA-NTWTRAALADLTRLVKELNADRDIYTLVVTGEGEKFFSA 64

Query: 65  GADISEMKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDIRIA 124
           GAD+    + +    R+      + F  L       IAA+NG+A+GGG E A++CDIRIA
Sbjct: 65  GADLKLFADGDKAMAREMARRFGEAFETLSAFRGVSIAAINGYAMGGGLECALACDIRIA 124

Query: 125 SSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNKVVE 184
              A+   PE  +G+ P  GGTQ L  LVG G AK++I   + + A+ ALRIGLV +VV 
Sbjct: 125 EEQAQMALPEAAVGLLPCAGGTQNLPWLVGEGWAKRMILCGERVNAETALRIGLVEEVVP 184

Query: 185 PSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTEDQKD 244
             +    A  +A +    +P +V  SKQ I       + T L  E E F + F T+DQ++
Sbjct: 185 RGQARERALALAQQAEKQSPSSVAASKQLIQGARHNPLGTILQTERELFVDLFDTQDQRE 244

Query: 245 AMTAFIEKR 253
            + AF+EKR
Sbjct: 245 GVQAFLEKR 253


Lambda     K      H
   0.317    0.134    0.365 

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: 178
Number of extensions: 10
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: 261
Length of database: 260
Length adjustment: 25
Effective length of query: 236
Effective length of database: 235
Effective search space:    55460
Effective search space used:    55460
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 (21.6 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