GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Burkholderia phytofirmans PsJN

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate BPHYT_RS28015 BPHYT_RS28015 enoyl-CoA hydratase

Query= reanno::Cup4G11:RR42_RS28545
         (384 letters)



>FitnessBrowser__BFirm:BPHYT_RS28015
          Length = 382

 Score =  327 bits (839), Expect = 3e-94
 Identities = 179/365 (49%), Positives = 222/365 (60%), Gaps = 5/365 (1%)

Query: 19  ADDEVRFDEINGIGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRGAGPKA 78
           A+ E+ F  +N + +ITLNRP  LNALS+ M+  L   +      D I A+VL+GAG K 
Sbjct: 15  AEREILFRVVNRVAIITLNRPAALNALSHAMVRELAVLVEHCRTDDGIVALVLKGAGAKG 74

Query: 79  FCAGGDIRALYDSFHAGTALHRQFFVDEYQLDYRLHCYPKPVVALMDGIVMGGGMGLAQA 138
           FCAGGD+R +        +    FFVDEY+LDY LH +PKPVVAL+DGI MGGGMGL Q 
Sbjct: 75  FCAGGDVREVQRLAKNNDSRWLAFFVDEYRLDYALHTFPKPVVALLDGIAMGGGMGLGQG 134

Query: 139 AHLRVLTERSRVAMPETGIGLVPDVGASHFLSKLPLALALYVGLTGVTLGAADTLLCKLA 198
           A LR++TERS++AMPET IG +PDVGA+ FLS +P  L LYVGLTG TL  AD L  +LA
Sbjct: 135 ARLRIVTERSKIAMPETRIGFLPDVGATRFLSVMPAELELYVGLTGATLSGADALRLQLA 194

Query: 199 DIAVPAASLEHFEQTLAAINRTGDVLADLRAALQATPDAGEQAAPLQSVLPAVLRHF--- 255
           D+ VPA  L  FE+ L  +   GD++A LR   +  P      APL +    +LRHF   
Sbjct: 195 DLCVPAEWLASFEERLQRMPLEGDLMAALRGVFE-PPCNIIPHAPLAAFTQLILRHFDRR 253

Query: 256 -RADASVAGLLDSLAAESDPAYADWAARTLDILRGRSPLMMAVTRELLLRGRDLDLADCF 314
              D  VA +   L  E       W   T D L G SP M+ VTRE LLRGR + LA+CF
Sbjct: 254 SSIDRMVATVRHDLLREPPREVKQWLQSTYDALTGHSPTMLYVTREALLRGRQMTLAECF 313

Query: 315 RMELGVVSHAFSQGDFIEGVRALIVDKDNAPRWRVKDASEVSEAVVQSFFDSPWPREPHP 374
           RMELG+V     +GDF EGVRA ++DKD   RW     +EV    V+ F  SPW  + HP
Sbjct: 314 RMELGIVKRVIEEGDFCEGVRAQLIDKDRKARWAPATLAEVRPERVRHFLASPWKSDAHP 373

Query: 375 LAMLG 379
           LA LG
Sbjct: 374 LAALG 378


Lambda     K      H
   0.322    0.137    0.405 

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: 383
Number of extensions: 15
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: 384
Length of database: 382
Length adjustment: 30
Effective length of query: 354
Effective length of database: 352
Effective search space:   124608
Effective search space used:   124608
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 (21.9 bits)
S2: 50 (23.9 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