GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Dyadobacter tibetensis Y620-1

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_025763144.1 X939_RS0110100 enoyl-CoA hydratase

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



>NCBI__GCF_000566685.1:WP_025763144.1
          Length = 275

 Score =  103 bits (257), Expect = 4e-27
 Identities = 77/246 (31%), Positives = 116/246 (47%), Gaps = 8/246 (3%)

Query: 17  ITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEMAE--RD 74
           I L RPE  NA    + +E+A  LA A    E R ++L+     F AGAD+    +   D
Sbjct: 31  IVLNRPEKRNAFTLTMAEEIAYALAYAHYSKEVRCLLLSARGPVFCAGADLNAFHDPASD 90

Query: 75  LVGILEDPRVAHWQRI----AAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQP 130
           LV     PR +   R+    A   KP IA V G  L GG  +      +I+  +A++  P
Sbjct: 91  LVNPTL-PRPSETVRLGDAFAGLLKPSIAQVEGAVLAGGFLMICGCTFVISVPEAQYSLP 149

Query: 131 EINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIERAL 190
           E+  GI P            G+ + M+M ++G+A  A  A   GL+++V       + A 
Sbjct: 150 EVKRGIWPMQVMASLDGLISGRKI-MEMAITGRAYSAAEALEMGLITQVVTHTEIQDTAE 208

Query: 191 AIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAFQEKR 250
            +A++I  +APLA++    A     +   A      +     L  +AD  EG+RAF+EKR
Sbjct: 209 ELAKLITSQAPLAIQEGMRAYADLHEMPSAERQGMLQQRLNTLLLSADAKEGVRAFREKR 268

Query: 251 RPEFTG 256
           RPE+ G
Sbjct: 269 RPEWKG 274


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: 183
Number of extensions: 10
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 257
Length of database: 275
Length adjustment: 25
Effective length of query: 232
Effective length of database: 250
Effective search space:    58000
Effective search space used:    58000
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