GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Rhizobium leguminosarum bv. trifolii WSM1325

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_012755571.1 RLEG_RS26045 crotonase/enoyl-CoA hydratase family protein

Query= CharProtDB::CH_091794
         (261 letters)



>NCBI__GCF_000023185.1:WP_012755571.1
          Length = 267

 Score =  183 bits (465), Expect = 3e-51
 Identities = 101/255 (39%), Positives = 144/255 (56%), Gaps = 4/255 (1%)

Query: 4   NNVILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFV 63
           + V+++    +A +T+NRP+ LNALN   +  +  ++  IE D  +  VILTG+GE++F 
Sbjct: 3   DTVLIDSRDGIATLTLNRPEKLNALNYALIDRLLAILDAIETDRSIRVVILTGSGERAFS 62

Query: 64  AGADISEMKEMNT----IEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSC 119
           AG DI E  E       +  R F   G ++  RLE   KPVIAAVNG A GGGCEI  + 
Sbjct: 63  AGGDIYEFSESVAQGADVAMRDFVARGQRLTARLEAYHKPVIAAVNGLAFGGGCEITEAV 122

Query: 120 DIRIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLV 179
            + IAS  A F +PE+ L + P FGGTQRL RL G   A +L+ T        AL +GLV
Sbjct: 123 PLAIASERALFAKPEINLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALELGLV 182

Query: 180 NKVVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFST 239
           N++V    LM  A ++A +I+ ++P+A      A+ RG+   I   L  E E F     T
Sbjct: 183 NQLVPHDALMPAAHDLARRILRHSPLAAASILTAVTRGINQSIAEGLLIEGEQFARMAPT 242

Query: 240 EDQKDAMTAFIEKRK 254
            D ++ + A+IE+RK
Sbjct: 243 ADLREGLDAWIERRK 257


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: 165
Number of extensions: 4
Number of successful extensions: 2
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: 267
Length adjustment: 25
Effective length of query: 236
Effective length of database: 242
Effective search space:    57112
Effective search space used:    57112
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 Apr 09 2024. 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