GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Limnohabitans curvus MWH-C5

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_108402835.1 B9Z44_RS06720 enoyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_003063475.1:WP_108402835.1
          Length = 268

 Score =  167 bits (422), Expect = 3e-46
 Identities = 97/264 (36%), Positives = 155/264 (58%), Gaps = 11/264 (4%)

Query: 3   FETIE-TKKEGNLFWITLNRPDKLNALNAKL-LEELDRAVSQAESDPEIRVIIITGKG-K 59
           + T+E T+   ++  + LNRP+  NALN ++ ++ LD  V   +   ++R +++TG G K
Sbjct: 9   YTTLECTQVSDHVLQVCLNRPEVGNALNTQMGVDLLDLWVRLTDVPGDLRCVVLTGAGAK 68

Query: 60  AFCAGADITQFNQLTPAEAWKFSKKGREIMDKIE----ALSKPTIAMINGYALGGGLELA 115
            FC G D+ + N +TP +AW++     EI +++      L  P I  ING+A GGGLE+A
Sbjct: 69  IFCGGGDLKERNGMTP-QAWQYQ---HEIFERLYWALIDLPLPVIGAINGHAYGGGLEMA 124

Query: 116 LACDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKY 175
           L CD   A+++A+  LPE+ LGI PG GGTQ L R +G+ RA E+ +TG     + A  +
Sbjct: 125 LCCDFLYASQDARFALPEVTLGIMPGMGGTQNLPRALGERRAKELALTGRPFSAEQALAW 184

Query: 176 GLVNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVV 235
           GLVN+V     +     + A++IA  +P+S+  IK+ +  G    L +    E   +  +
Sbjct: 185 GLVNQVAAPDAVLALALETAQRIAANAPLSVRQIKKSIRYGGQMELRTAYRFEVEAYNRL 244

Query: 236 FSTEDKKEGVSAFLEKREPTFKGK 259
             T+D++EGV+AF +KR P FKG+
Sbjct: 245 VDTDDRREGVAAFNDKRPPVFKGR 268


Lambda     K      H
   0.315    0.135    0.382 

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: 172
Number of extensions: 13
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: 259
Length of database: 268
Length adjustment: 25
Effective length of query: 234
Effective length of database: 243
Effective search space:    56862
Effective search space used:    56862
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: 42 (22.0 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