Alignments for a candidate for hcrA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Paraburkholderia bryophila 376MFSha3.1

Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate H281DRAFT_02182 H281DRAFT_02182 xanthine dehydrogenase, molybdenum binding subunit apoprotein

Query= SwissProt::O33819
         (769 letters)



>FitnessBrowser__Burk376:H281DRAFT_02182
          Length = 795

 Score =  305 bits (781), Expect = 6e-87
 Identities = 245/804 (30%), Positives = 375/804 (46%), Gaps = 58/804 (7%)

Query: 8   HGTVGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEG 67
           H  +G      +    +TG  +YT DI  P       LRSPHAHA+I +IDT+AA+   G
Sbjct: 7   HSLIGASVERKEDYRFLTGNGQYTDDILLPQQTYAVFLRSPHAHAKINSIDTTAAKQSPG 66

Query: 68  VIAVCTGAETP------VPFGVL-------PIAENEYPL-ARDKVRYRGDPVAAVAAIDE 113
           V+A+ TGA+        +P G L       P+ E  +P+ A  KVR+ GD VA V A   
Sbjct: 67  VVAIFTGADMAAENVGGLPCGWLIHSTDGKPMNEPPHPIIAHTKVRHVGDQVALVIADSI 126

Query: 114 VTAEKALALIKVDYEVLPAYMTPKAAMKAGAIALHDDKPNNILREV-HAEFGDVAAAFAE 172
             A+ A  LI+VDY+VLPA +    A  AG  A+HD+ P+N+     H +     AAFA+
Sbjct: 127 KAAKDAAELIEVDYDVLPAVVDTAHAADAGQPAVHDEVPDNVCYNWGHGDKAATDAAFAK 186

Query: 173 ADLIREKTYTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAA-CLQMDS 231
           A  +         +    +E  A  A Y    D  TL    Q P+   L +AA  L +  
Sbjct: 187 AAHVTTLDIVNNRLVPNAIEPRAVNASYSSQDDSYTLYVANQNPHVERLLMAAFVLSLPE 246

Query: 232 ARIRVIKPFLGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTEVK 291
           +++RVI P +GGGFG++      ++     ++K +  V+    R E F++         K
Sbjct: 247 SKLRVIAPDVGGGFGSKIFLYAEDVALTWASKKIRRPVKWTAERSEAFLSDAHGRDHVTK 306

Query: 292 MKIGLKKDGKIAALALEATQAGGAYAGY---GIITILYTGALMHGLYHIPAIKHDAWRVY 348
            ++ +  DGK  A+ +      GAY       + TILY   L+ G Y  PAI  +   V+
Sbjct: 307 AELAMDADGKFLAMRIHTIANMGAYLSTFASSVPTILYA-TLLAGQYATPAIYAEVKAVF 365

Query: 349 TNTPPCGAMRGHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRVMS 408
           TNT P  A RG G  +     E L+     E+ +D  +IR+ N + + PY T      ++
Sbjct: 366 TNTVPVDAYRGAGRPEATYVVERLVETAAREMKLDPAEIRRRNFIREFPYATPVG---LT 422

Query: 409 YGVPECLEKVKAAS-------GWEERKGKLPK-GRGLGIALSHFVSGTS-TPKHWTGEPH 459
           Y   +  E + A S       G+E R+ +  + G+  G+  S ++      P +  G   
Sbjct: 423 YDTGD-YETILARSLELADVKGFEARRQESERNGKRRGLGYSCYIEACGLAPSNIAGALG 481

Query: 460 ATVNL------KLDFDGGITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSAL 513
           A   L      ++   G +T+ TG+   GQG  T  +QV A+ LG+ L  + ++  D+  
Sbjct: 482 ARAGLFEVGQIRVHPTGSVTVFTGSHSHGQGHETTFAQVVADRLGLPLESVEIVHGDTGR 541

Query: 514 TPKDNGSYSSRVTFMVGNASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQD 573
            P   G+Y SR   + G+A + A ++++    K AA  L+A  EDIE  D +F V+G+ D
Sbjct: 542 IPFGMGTYGSRSIAVGGSAIMKALDKIETKAKKIAAHLLEAATEDIEFKDGVFRVAGT-D 600

Query: 574 PGLSFQEVVKAAMVDSGTITVKGTYTCPTEFQGDKKIRGSAIGATMGFCY--AAQVVEAS 631
              +F E+  AA V          +  P +   +  +  SA      F Y   A + E  
Sbjct: 601 RTKAFAEISLAAYV---------PHNYPLDVL-EPGLEESAFYDPSNFTYPSGAYICEVE 650

Query: 632 VDEITGKVTAHKVWVAVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVYDN--GRMVHG 689
           VD  TG     +     D G  +NP+ VEGQ  GG+  G+GQA+ E  VYDN  G+++ G
Sbjct: 651 VDPDTGVCRIQRFTAVDDFGNVINPMIVEGQVHGGLGQGIGQAMLERCVYDNESGQLLSG 710

Query: 690 NILDYRVPTIVESPDIEVIIVESMD-PNGPFGAKEASEGMLAGFLPAIHEAVYEA---VG 745
           + +DY +P   + PD  V   +     + P G K   E    G  PA+  A+ +A   +G
Sbjct: 711 SYMDYAMPHASDLPDFTVETAKGTPCTHNPLGVKGCGEAGAIGSPPAVINAIIDALAPLG 770

Query: 746 VRATDFPLSPDRITELLDAKEAAA 769
           V     P +P R+   + A + AA
Sbjct: 771 VTDLQMPATPHRVWSAIHAVKQAA 794


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: 1426
Number of extensions: 60
Number of successful extensions: 8
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: 795
Length adjustment: 41
Effective length of query: 728
Effective length of database: 754
Effective search space:   548912
Effective search space used:   548912
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources