Alignments for a candidate for hcrA in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Magnetospirillum magneticum AMB-1

Align 4-hydroxybenzoyl-CoA reductase HbaC subunit (EC 1.3.7.9) (characterized)
to candidate WP_011386063.1 AMB_RS18770 xanthine dehydrogenase family protein molybdopterin-binding subunit

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



>NCBI__GCF_000009985.1:WP_011386063.1
          Length = 732

 Score =  235 bits (600), Expect = 6e-66
 Identities = 229/766 (29%), Positives = 329/766 (42%), Gaps = 74/766 (9%)

Query: 18  VDGIDKVTGRARYTADLDHTGALVARILRSPISHGDIVRLDVSKALALDGVAAIVTGEDC 77
           V+ +  +TG   YT D++ TG     ++RS + H D+  +D   A A+ GV  ++T  + 
Sbjct: 13  VEDLRFLTGGGCYTDDINLTGQSYGMVVRSLLPHADVT-VDAVAARAMPGVLLVLTAAEM 71

Query: 78  A------ITYGVLPI-AMNEYP---MARDRVRYRGEPVAAVAAVDAETARQALDLIELEL 127
           A      +  G LP  A+  +P   +A  R R+ GEP+A V A     AR A + + ++ 
Sbjct: 72  AEQGIGPMVCGFLPEDAVPRHPRPVIAGPRTRHAGEPLAFVVAETLAQARDAAEAVLVDY 131

Query: 128 RELPAYYESEAARAPDAWLLHDNKPGNIEREVHNEFGDLAAGFEAADLIRTHTHHCAEVN 187
             LPA          DA++    + G+  R V   F   A   E  DLI       A   
Sbjct: 132 HPLPA-------TPHDAFVW---EMGDASR-VAEAFARAARVVEL-DLINNRLAPTA--- 176

Query: 188 HAQIEPHACLMDYDPVTGRLTAQSVSQVGYYLHLMLARCLEIDPSRVRVIKPFVGGGFGA 247
              +EP ACL    P  GRL   + SQ  + +   LA  L I   R+ VI P VGGGFG 
Sbjct: 177 ---MEPRACLARPLP-GGRLELTAGSQGVHEIRDRLAPVLGIAADRLDVITPDVGGGFGL 232

Query: 248 RVEVLNFEVIAALLARKASGRVLMRLSREETFITHRARPQTDITLTIGTRRDGRFTACSC 307
           ++     + +A + AR     V     R E+F++         T  +    +GRF     
Sbjct: 233 KISPFPEQAMALVAARILDRPVKWTGDRTESFLSDTHGRGHLSTARLALDAEGRFLGLQV 292

Query: 308 EVVQRGGAY-AGYGIVTILYAGA-LLQGLYDIPAVKYDGYRVYTNLPPCGAMRGHGSVDV 365
           E V   GAY + YG      AG  +L G+YDIPA       ++T+  P  A RG G  + 
Sbjct: 293 ETVADLGAYISNYGAFVPTLAGTGMLTGVYDIPAFHARVRAIHTHTTPVDAYRGAGRPEA 352

Query: 366 RHAFENLVDRMARELGLDPFAVRRANLL---AAPTRTLNDLMVNSYGLAECLDKVERASG 422
            +  E LVD  A + GL P  +R+ N +   A P  +      +S   A  +D+    SG
Sbjct: 353 AYCIERLVDAAAHDTGLSPVEIRKRNFIPPDAFPYASAGRHTYDSGEFARVMDRALERSG 412

Query: 423 WHERIGRLPPG------KGLGMACSHYVSGSAKPIHFTGEPHAVVALRLDFDGGITALTG 476
           W +   R          +G+G+A    + G       +GE    V L L  DGG   L G
Sbjct: 413 WADFASRQADSTARGRKRGIGLAYYIEICGGT-----SGED---VTLTLSPDGGAEILVG 464

Query: 477 AADIGQGSSTVVAITVAETLGVALNRVRVISGDSAITPKDNGAYSSRITFMVGNAAIDAA 536
               GQG  T  A  VA  LG+A+ RVRVI GD+       G   SR     G A   A 
Sbjct: 465 TQSNGQGHETAYAQMVAAELGLAIERVRVIQGDTRRIGTGGGTGGSRSLSQQGGAIASAV 524

Query: 537 TKLKQILIAAAARKLEAVPEQIECAGESFFIGSGAQAALGFAEVVKAALVDEGAITVKGI 596
               + L   AAR L+A   + +     F+  +G   ++ FA+V+  A   E  +     
Sbjct: 525 ESFIEHLQPQAARLLQAERAEFDA---GFYRAAG--GSVSFAQVLAEA---ETPLAASLR 576

Query: 597 FTCPPESQGGQHRGGAVGSTMGFSYAAQVVEVSVDDATGLITVDKVWAALDCGRAINPLA 656
           F  P  +               F     V EV VD  TG   + +     D G  +NPL 
Sbjct: 577 FRPPAAT---------------FPNGCHVCEVEVDPETGETEIVRYTIVDDVGTVLNPLL 621

Query: 657 VVGQVQGAVWMGMGQAMCEETRY--LDGLPAHASFLEYRMPTMIESPPIEVAIVESVDPF 714
           + GQ+ G    G+GQA+ E   +      P  +S ++Y +P     P I+ + VE     
Sbjct: 622 LKGQIVGGAVQGIGQALLEHAVFDPESTQPLTSSLIDYAVPRAAHIPEIDFSTVEIPCRT 681

Query: 715 GPFGAKEASEGALAGFPPAMVNAVANAIGIDLDDLPATPDRVVEAL 760
            P G K A E    G  PA++NA+ NA+ +   D+PATP  V  AL
Sbjct: 682 HPLGLKGAGEAGTIGAAPAVINALCNALELRHMDMPATPLAVWNAL 727


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: 1421
Number of extensions: 78
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: 777
Length of database: 732
Length adjustment: 40
Effective length of query: 737
Effective length of database: 692
Effective search space:   510004
Effective search space used:   510004
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 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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