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_012760683.1 RLEG_RS34755 carnitinyl-CoA dehydratase

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



>NCBI__GCF_000023185.1:WP_012760683.1
          Length = 260

 Score =  117 bits (292), Expect = 3e-31
 Identities = 84/251 (33%), Positives = 127/251 (50%), Gaps = 8/251 (3%)

Query: 13  GVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGS-RKAFAAGADIKEMA 71
           GV  + + RP+A NA++      L         D   R  +++G+  K F AG D+K  A
Sbjct: 12  GVLEVVIDRPKA-NAIDLATSRALGLIFRNFRDDPALRVAIVSGAGEKFFCAGWDLKAAA 70

Query: 72  ERDLV-GILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQP 130
             D V G          Q +   +KP+I AVNG C GGG E+A+ AD+++A E A F  P
Sbjct: 71  SGDAVDGDYGVGGFGGLQELRDLNKPVICAVNGICCGGGLEIALSADLILAAEHATFALP 130

Query: 131 EINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIERAL 190
           EI  G +  A    +L + +   +AM M+L+G+ +D   A R G ++EV   E  +ERA 
Sbjct: 131 EIRSGTVADAASI-KLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFINEVLPAERLMERAW 189

Query: 191 AIARVIAQKAPLAVRLAKEALLKAEDTDLASGLR--FERHAFTV--LAGTADRAEGIRAF 246
            +AR++     L     KE + +AE +   + +    +R   TV  L  + D+ EG RAF
Sbjct: 190 ELARLLESGPSLVHAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYSSEDQLEGARAF 249

Query: 247 QEKRRPEFTGR 257
            EKR P + G+
Sbjct: 250 AEKRSPIWKGK 260


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: 159
Number of extensions: 9
Number of successful extensions: 4
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: 260
Length adjustment: 24
Effective length of query: 233
Effective length of database: 236
Effective search space:    54988
Effective search space used:    54988
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