Alignments for a candidate for hcrA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Burkholderia phytofirmans PsJN

Align 4-hydroxybenzoyl-CoA reductase HbaC subunit (EC 1.3.7.9) (characterized)
to candidate BPHYT_RS10835 BPHYT_RS10835 carbon monoxide dehydrogenase

Query= metacyc::MONOMER-17404
         (777 letters)



>FitnessBrowser__BFirm:BPHYT_RS10835
          Length = 1012

 Score =  259 bits (663), Expect = 4e-73
 Identities = 239/804 (29%), Positives = 341/804 (42%), Gaps = 55/804 (6%)

Query: 24  VTGRARYTADLD-HTGALVARILRSPISHGDIVRLDVSKALALDGVAAIVTGEDCAITYG 82
           +TG  RY  D+    G L A ILRSP +H ++V +D   A  L GV AI+T +D      
Sbjct: 42  LTGHGRYGDDIGIRPGTLHAAILRSPHAHAELVSIDTDAASKLPGVHAILTRDDLRAWSR 101

Query: 83  VLPIA----MNEYPMARDRVRYRGEPVAAVAAVDAETARQALDLIELELRELPAYYESEA 138
              +     M ++ +A DRVRY GEPVA V A     A   LDL+++E   L      E 
Sbjct: 102 PFVVGVKSPMEQWALAMDRVRYVGEPVAVVLAQSRAIAEDGLDLLKVEYATLDPVTSIEQ 161

Query: 139 ARAPDAWLLHDNKPGNIEREVHNEFGDLAAGFEAADLIRTHTHHCAEVNHAQIEPHACLM 198
           A + ++ +LH+    N+  + H  +G+  A FE A        H      A IE    + 
Sbjct: 162 AASDESPVLHEKVGSNVISDRHFRYGEPEAAFEKAPHRVKLVAHYPRNTCAPIECGVVIA 221

Query: 199 DYDPVTGRLTAQSVSQVGYYLHLMLARCLEIDPSRVRVIKPF-VGGGFGARVEVLNFEVI 257
           +Y          S     + LH ++A  L +  +R+R   P   GG FG +  V  + V+
Sbjct: 222 EYLAGDEGYDVTSNFMGPFSLHAVMAMALNVPANRLRHKAPRDSGGSFGVKQAVFPYVVL 281

Query: 258 AALLARKASGRVLMRLSREETFITHRARPQTDITLTIGTRRDGRFTACSCEVVQRGGAYA 317
             L +RKA   V     R E      +      TL      DGR TA S + ++  G Y 
Sbjct: 282 MCLASRKAGAPVKWVEDRFEHLSAATSATARLSTLEAAVESDGRITALSYDQLEDCGGYL 341

Query: 318 GYGIVTILYA-GALLQGLYDIPAVKYDGYRVYTNLPPCGAMRGHGSVDVRHAFENLVDRM 376
                   Y     L G Y I  +      V TN  P G +RG G   V  A E L+ R+
Sbjct: 342 RAPEPATFYRMHGCLTGAYAIDNLLVRNRVVLTNKTPTGLVRGFGGPQVYFALERLMQRI 401

Query: 377 ARELGLDPFAVRRANLLAA---PTRTLNDLMVNSYGLAECLDKVERASGWHERIGRLPPG 433
           A EL LD   V R N +AA   P R     +++S    E L +     G+ E   R    
Sbjct: 402 ALELKLDVLDVYRRNFVAADAFPYRAAAGALLDSGNYQEALRRALAEGGYDELRARRDAA 461

Query: 434 K------GLGMACSHYVSGSAKPIHFTGEPH-------------AVVALRLDFDGGITAL 474
           +      G+G A     S S      T  P              A   + +D  GG+   
Sbjct: 462 RKEGRLYGIGFAAIVEPSVSNMGYITTVMPAEARKKAGPKSGAIASATVSVDLLGGVVVT 521

Query: 475 TGAADIGQGSSTVVAITVAETLGVALNRVRV-ISGDSAITPKDN-----GAYSSRITFMV 528
             +   GQG  TV A  VA+ LGV+ + V V +  D   T KD      G YSSR    V
Sbjct: 522 IASTPAGQGHMTVCAQVVADVLGVSPHDVVVNVEFD---THKDAWSVAAGNYSSRFAGAV 578

Query: 529 GNAAIDAATKLKQILIAAAARKLEAVPEQIECAGESFFIGSGAQ-AALGFAEVVKAALVD 587
                 AA +++  +    ++++   PE I C  E      GA+  A  F  V   A   
Sbjct: 579 AGTVHLAAVRVRDKIARIVSKQMGCAPEDI-CFEEGRIFAKGAEDRAQPFGRVAANAPHW 637

Query: 588 EGAITVKG--------IFTCPPESQGGQHRGGAVGSTMGFSYAAQVVEVSVDDATGLITV 639
             A+  +G        +F  PP +         V ++  + +A  +  V +D ATG + +
Sbjct: 638 APALLPEGEEPGLRETVFWNPP-NMAAPDENDRVNTSAAYGFAFDMCGVELDRATGRVRI 696

Query: 640 DKVWAALDCGRAINPLAVVGQVQGAVWMGMGQAMCEETRY-LDGLPAHASFLEYRMPTMI 698
           D+   A D G  +NP    GQ++GA   G+G A+ EE RY  DG     +  +Y MPT  
Sbjct: 697 DRYVTAHDAGTLLNPALADGQIRGAFAQGLGAALMEEFRYGSDGSFQSGTLADYLMPTTC 756

Query: 699 ESPPIEVAIVESVDPFGPFGAKEASEGALAGFPPAMVNAVANAIGIDLDDLPATPDRVVE 758
           E P   +  +E+  PF P GAK   EG     PP + NAVA+A+G+D   LP TP +V+ 
Sbjct: 757 EVPDPVIVHLETPSPFTPLGAKGLGEGNNMSTPPCIANAVADALGVDDIRLPLTPSKVMA 816

Query: 759 ALA-----RRRREAKRAVAVRAAS 777
            +        R E + A A + A+
Sbjct: 817 LIGIDDPEPSRPEFREAPAAKPAT 840


Lambda     K      H
   0.320    0.136    0.402 

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: 1890
Number of extensions: 98
Number of successful extensions: 9
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: 777
Length of database: 1012
Length adjustment: 43
Effective length of query: 734
Effective length of database: 969
Effective search space:   711246
Effective search space used:   711246
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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