GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Dyella japonica UNC79MFTsu3.2

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate N515DRAFT_1164 N515DRAFT_1164 enoyl-CoA hydratase

Query= reanno::Phaeo:GFF1711
         (348 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1164
          Length = 260

 Score =  100 bits (248), Expect = 5e-26
 Identities = 85/247 (34%), Positives = 113/247 (45%), Gaps = 18/247 (7%)

Query: 3   DIDIRITGRAGRITLTRSKALNALSYDMCMAVDAALKAWADDDAVDLVVMDAEGEKAFCA 62
           ++DI   G    IT+ R   LNAL+ D    +  A    A DDAV  VV+   G+KAF A
Sbjct: 5   NLDIGNRGAVRIITVNRPDKLNALNRDTLNELTLAFAQAAQDDAVRTVVLAGAGDKAFVA 64

Query: 63  GGDIAELYQTGTSGDYDYGRRFWRDEYRMNARIFEYPKPVLSFLQGFVMGGGVGLGCHGT 122
           G DIAE+   G +     G  F R   R+ + I    KPV++ +QGF +GGG+ L     
Sbjct: 65  GADIAEM--NGYTPVQAQG--FSRAGQRLMSSIERLGKPVVARIQGFALGGGMELAMACH 120

Query: 123 HRIVGDSTKIAMPEVGIGLIPDVGGTLMLALAPGR-LGEYLGLTGARMTAADAIYAGFAD 181
            R+  +  +   PE+ +GLIP  GGT  L    GR     L LTGA + A  A   G  +
Sbjct: 121 LRVASEKARFGQPEINLGLIPGFGGTQRLLRLAGRGAALELCLTGAMVGAQRAYELGVVN 180

Query: 182 HYVPETRWPNLISELEQTGRADLLAESAETAPAGTLAPMYDDIGRNFGGETLTDILTALD 241
             V        +  L     AD LA SA  A AG L  +        GGE   D    L+
Sbjct: 181 RVVAPEALDETVDAL-----ADQLAASAPLAAAGILDAILQ------GGEMALD--QGLE 227

Query: 242 HDDSSFA 248
            +  +FA
Sbjct: 228 FETQAFA 234


Lambda     K      H
   0.320    0.137    0.406 

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: 170
Number of extensions: 6
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: 348
Length of database: 260
Length adjustment: 27
Effective length of query: 321
Effective length of database: 233
Effective search space:    74793
Effective search space used:    74793
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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