GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcrA in Burkholderia phytofirmans PsJN

Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate BPHYT_RS01765 BPHYT_RS01765 carbon-monoxide dehydrogenase

Query= SwissProt::O33819
         (769 letters)



>FitnessBrowser__BFirm:BPHYT_RS01765
          Length = 793

 Score =  300 bits (769), Expect = 2e-85
 Identities = 243/801 (30%), Positives = 370/801 (46%), Gaps = 58/801 (7%)

Query: 6   PQHGTVGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEAL 65
           P    +G      +    +TG  +YT DI  P       LRSPHAHA+I +IDT+AA+  
Sbjct: 4   PDTHLIGASVERKEDYRFLTGNGQYTDDIVLPQQTYAIFLRSPHAHAKINSIDTAAAKQS 63

Query: 66  EGVIAVCTGAETP------VPFGVL-------PIAENEYPL-ARDKVRYRGDPVAAVAAI 111
            GV+A+ TGA+        +P G L       P+ E  +P+ A  KVR+ GD VA V A 
Sbjct: 64  PGVVAIFTGADMAADNVGGLPCGWLIHSTDGKPMNEPPHPIIAHTKVRHVGDQVALVIAD 123

Query: 112 DEVTAEKALALIKVDYEVLPAYMTPKAAMKAGAIALHDDKPNNILREV-HAEFGDVAAAF 170
               A+ A  LI+VDY+VLPA +    A  AG  A+HD+ P+NI     H +     AAF
Sbjct: 124 SIKAAKDAAELIEVDYDVLPAVVDTAHAADAGQPAVHDEVPDNICYNWGHGDKAATDAAF 183

Query: 171 AEADLIREKTYTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAA-CLQM 229
           A+A  +         +    +E  A  A Y    D  TL    Q P+   L +AA  L +
Sbjct: 184 AKAAHVTTLDIVNNRLVPNAIEPRAVNASYSVQDDSYTLYVANQNPHVERLLMAAFVLSL 243

Query: 230 DSARIRVIKPFLGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTE 289
             +++RVI P +GGGFG++      ++     ++K +  V+    R E F++        
Sbjct: 244 PESKLRVIAPDVGGGFGSKIFLYAEDVALTWASKKIRRPVKWTAERSEAFVSDAHGRDHV 303

Query: 290 VKMKIGLKKDGKIAALALEATQAGGAYAGY---GIITILYTGALMHGLYHIPAIKHDAWR 346
            K ++ +  DGK   + +  T   GAY       + TILY   L+ G Y  PAI  +   
Sbjct: 304 TKAELAMDADGKFLGMRIHTTANMGAYLSTFASSVPTILYA-TLLAGQYATPAIYAEVKA 362

Query: 347 VYTNTPPCGAMRGHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRV 406
           V+TNT P  A RG G  +     E L+     ++ +D  +IR+ N + + PY T      
Sbjct: 363 VFTNTVPVDAYRGAGRPEATYVVERLVETAARDMKLDPAEIRRRNFIREFPYATPVG--- 419

Query: 407 MSYGVPEC---------LEKVKAASGWEERKGKLPKGRGLGIALSHFVSGTSTPKHWTGE 457
           ++Y   +          L  VK  +  ++   K  K RGLG +      G + P +  G 
Sbjct: 420 LTYDTGDYETILARSLELADVKGFAARKQESEKNGKLRGLGYSCYIEACGLA-PSNIAGA 478

Query: 458 PHATVNL------KLDFDGGITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADS 511
             A   L      ++   G +T+ TG+   GQG  T  +QV A+ LG+ L  + ++  D+
Sbjct: 479 LGARAGLFEVGQIRVHPTGSVTVFTGSHSHGQGHETTFAQVVADRLGIALESVEIVHGDT 538

Query: 512 ALTPKDNGSYSSRVTFMVGNASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGS 571
              P   G+Y SR   + G+A + A ++++    K AA  L+A  EDIE  D +F V+G+
Sbjct: 539 GRIPFGMGTYGSRSIAVGGSAIMKALDKIETKAKKIAAHLLEAAAEDIEFKDGVFRVAGT 598

Query: 572 QDPGLSFQEVVKAAMVDSGTITVKGTYTCPTEFQGDKKIRGSAIGATMGFCY--AAQVVE 629
            D   +F ++  AA V          +  P +   +  +  SA      F Y   A + E
Sbjct: 599 -DRTKAFADISLAAYV---------PHNYPLDVL-EPGLEESAFYDPTNFTYPSGAYICE 647

Query: 630 ASVDEITGKVTAHKVWVAVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVYDN--GRMV 687
             VD  TG     +     D G  +NP+ VEGQ  GG+  G+GQA+ E  VYDN  G+++
Sbjct: 648 IEVDPETGVCRIQQFTAVDDFGNVINPMIVEGQVHGGLAQGIGQAMLERCVYDNESGQLL 707

Query: 688 HGNILDYRVPTIVESPDIEVIIVESMD-PNGPFGAKEASEGMLAGFLPAIHEAVYEA--- 743
            G+ +DY +P   + P+  V  V+     + P G K   E    G  PA+  A+ +A   
Sbjct: 708 SGSYMDYAMPHASDLPNFTVETVKGTPCTHNPLGVKGCGEAGAIGSPPAVINAILDALAP 767

Query: 744 VGVRATDFPLSPDRITELLDA 764
           +GV     P +P R+   + A
Sbjct: 768 LGVTDLQMPATPHRVWSAIHA 788


Lambda     K      H
   0.317    0.134    0.386 

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: 1434
Number of extensions: 58
Number of successful extensions: 7
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: 769
Length of database: 793
Length adjustment: 41
Effective length of query: 728
Effective length of database: 752
Effective search space:   547456
Effective search space used:   547456
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: 41 (21.7 bits)
S2: 55 (25.8 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