GapMind for catabolism of small carbon sources

 

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

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_012755571.1 RLEG_RS26045 crotonase/enoyl-CoA hydratase family protein

Query= metacyc::MONOMER-15953
         (257 letters)



>NCBI__GCF_000023185.1:WP_012755571.1
          Length = 267

 Score =  169 bits (429), Expect = 4e-47
 Identities = 106/263 (40%), Positives = 149/263 (56%), Gaps = 8/263 (3%)

Query: 1   MPHTLSVDAPEQGVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGS-RK 59
           M  T+ +D+ + G+  +TL RPE LNALN  L+D L A L   E D   R V+LTGS  +
Sbjct: 1   MADTVLIDSRD-GIATLTLNRPEKLNALNYALIDRLLAILDAIETDRSIRVVILTGSGER 59

Query: 60  AFAAGADIKEMAERDLVGILEDPR--VAHWQRIAA----FSKPLIAAVNGFCLGGGCELA 113
           AF+AG DI E +E    G     R  VA  QR+ A    + KP+IAAVNG   GGGCE+ 
Sbjct: 60  AFSAGGDIYEFSESVAQGADVAMRDFVARGQRLTARLEAYHKPVIAAVNGLAFGGGCEIT 119

Query: 114 MHADILIAGEDARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRA 173
               + IA E A F +PEINL + P  GGTQRL R  G+  A++++L+G A   + A   
Sbjct: 120 EAVPLAIASERALFAKPEINLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALEL 179

Query: 174 GLVSEVTLPELTIERALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVL 233
           GLV+++   +  +  A  +AR I + +PLA      A+ +  +  +A GL  E   F  +
Sbjct: 180 GLVNQLVPHDALMPAAHDLARRILRHSPLAAASILTAVTRGINQSIAEGLLIEGEQFARM 239

Query: 234 AGTADRAEGIRAFQEKRRPEFTG 256
           A TAD  EG+ A+ E+R+P + G
Sbjct: 240 APTADLREGLDAWIERRKPNYPG 262


Lambda     K      H
   0.320    0.134    0.374 

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: 206
Number of extensions: 11
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: 267
Length adjustment: 25
Effective length of query: 232
Effective length of database: 242
Effective search space:    56144
Effective search space used:    56144
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 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