Alignments for a candidate for hcrA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Stenotrophomonas chelatiphaga DSM 21508

Align 4-hydroxybenzoyl-CoA reductase, α subunit (EC 1.3.7.9) (characterized)
to candidate WP_057507661.1 ABB28_RS05445 xanthine dehydrogenase family protein molybdopterin-binding subunit

Query= metacyc::MONOMER-14376
         (794 letters)



>NCBI__GCF_001431535.1:WP_057507661.1
          Length = 732

 Score =  226 bits (576), Expect = 3e-63
 Identities = 232/783 (29%), Positives = 337/783 (43%), Gaps = 99/783 (12%)

Query: 21  VGARLPLIDGVEKVTGTARYT------ADLPAQGALVGKLLRSPYAHAELLEVDISEALK 74
           VG  L  IDG +K TG ARY       A  PA G +VG    +  A   +  +++  A  
Sbjct: 18  VGKPLDRIDGPQKTTGHARYAYEWHDVAASPAYGYVVG----AGIAKGRVTAMELDAARA 73

Query: 75  LPGVRGIVTGNDCDTPYGVIPIAQNEFPLARG-RIRYVGEPVAAVAAVDEATTDAALALI 133
            PGV  IVT ++  T +      +N  PL  G ++ +  + +A V A       AA  L+
Sbjct: 74  SPGVLAIVTADNAGTLHKG---DRNTAPLLGGPKVDHYHQALALVVAETFEQARAAADLV 130

Query: 134 RLKVRELPAYFDAADARKADVVLLH---DNKKGNIEREVHNEFGDAAAGFAAADLICEET 190
           R++       FD   A+KA   L     D + GN E+     +GDA     A       T
Sbjct: 131 RIRYAPTKGVFDLDAAKKAGNPLQDTDPDARVGNFEKA----YGDAPVTLDA-------T 179

Query: 191 FECAEVHHAMMEPNASLAAWDNERGHLTLWSVTQVPYYVHESLARCMKLDAAYIRVIKPF 250
           +   +  HAMMEP+ASLAAWD ++  LT+W+  Q+  +  + LA  + L    +R++ P+
Sbjct: 180 YHTPDQSHAMMEPHASLAAWDGDQ--LTVWTSNQMIAWGKKDLATTLGLPEDKVRLVSPY 237

Query: 251 VGGGFGHRVETLNFEIIAGLLARAARGTVRLLQTREEAFLTHRGRPQTYVRMKLGLTRDG 310
           +GGGFG ++   +  ++A L ARAA+  V+L   R         RP T  R++LG T +G
Sbjct: 238 IGGGFGGKLFIRSDVVLAALGARAAKRPVKLALQRPLIANNTTHRPATVQRIRLGATAEG 297

Query: 311 RMTACEAEV----VQRGGAYGGYGLVTILYAGALLNGLYDLPAVKYDGYRVYT-NTPPCG 365
            +TA   E     +  G          +LYAG          A +  G R++T + P   
Sbjct: 298 TLTAIGHESWSGNLSGGSPEEAVQQTKLLYAG----------ANRLAGLRLHTVDLPEGN 347

Query: 366 AMRGHGTVNIRFAFESLLDMMAAELGLDAFAVRRRNLLKAPTETINGLKVMSY-GLPECL 424
           AMR  G      A E  +D MA +L LD    R RN      +  N  +  S   L +CL
Sbjct: 348 AMRAPGEAPGLMALEIAMDEMAEKLKLDPVEFRIRN--DTQVDPSNPERPFSQRQLVQCL 405

Query: 425 DWVEQASGWRERAARLEANSDGPIRRGIGIAC---SHFVSGSAKPVHFTGQPHATIALRV 481
               Q  GW +R+A      DG    G+G+A    ++ V  S   V            R+
Sbjct: 406 QDGAQRFGWDKRSAVPAQRRDGRWLVGMGVAAGFRNNLVMKSGARV------------RL 453

Query: 482 DFDAGITILTGASDIGQGSSTIITQVVAEILGVEYRRLRLIATDSALTPKDNGSYSSRVT 541
           D    +T+ T  +DIG GS TI+ Q  AE+LGV   ++ +   DS+  P   GS      
Sbjct: 454 DSKGHVTVETDMTDIGTGSYTILGQTAAEMLGVTLDQVTVKLGDSSF-PASAGS------ 506

Query: 542 FMVGNAAADAARNLKAVLVAAAAKRLQVAEA-----DVDWLGEAAAVVGDASRQIPFHDI 596
                       N     V AA  +L+ A A     D D    A   V D +R       
Sbjct: 507 ------GGQWGANSATAGVFAACTKLRAAIAGKLGYDADTATFADGKVRDGNRS------ 554

Query: 597 VEEALVDVGMLTVKGTFTCPPEFQGGKQRGGAVGSTMGFSYAAQAVEVSVDTELGKVTVE 656
                  +G     G        +          ST    +AA  VEV VD   G+  + 
Sbjct: 555 -----AALGKAAADGELVAEDSIEFATLEEKYQQST----FAAHFVEVGVDVATGESRIR 605

Query: 657 KVWSAIDCGFAINPMSVEGQVQGAIWMGMGQAISEETVYEN--GRHKAVSLLDYRVPTII 714
           ++ +    G  +NP +   QV GA+ MG+G A+SEE   +   G      L  Y VP   
Sbjct: 606 RMLAVCAAGRILNPKTARSQVIGAMTMGIGAALSEELAVDTRLGFFVNHDLAGYEVPVHA 665

Query: 715 ESPDIAVHIVESLDP-NGPFGAKEASEGPLAGVMSAIAAAIEDATGTRIRATPFTPDRVF 773
           + P   V  ++  D  + P  AK   E  L GV +A+A AI +ATG R+R+ P T D++ 
Sbjct: 666 DVPHQEVVFLDEADAISSPMKAKGVGELGLCGVSAAVANAIYNATGVRVRSYPITLDKLL 725

Query: 774 DAL 776
             L
Sbjct: 726 GGL 728


Lambda     K      H
   0.319    0.135    0.397 

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: 1230
Number of extensions: 54
Number of successful extensions: 10
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: 794
Length of database: 732
Length adjustment: 40
Effective length of query: 754
Effective length of database: 692
Effective search space:   521768
Effective search space used:   521768
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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