Alignments for a candidate for hcrA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Escherichia coli BW25113

Align 4-hydroxybenzoyl-CoA reductase, α subunit (EC 1.3.7.9) (characterized)
to candidate 16946 b2866 xanthine dehydrogenase, molybdenum binding subunit (NCBI)

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



>FitnessBrowser__Keio:16946
          Length = 752

 Score =  357 bits (917), Expect = e-102
 Identities = 242/762 (31%), Positives = 386/762 (50%), Gaps = 35/762 (4%)

Query: 28  IDGVEKVTGTARYTADLPAQGALVGKLLRSPYAHAELLEVDISEALKLPGVRGIVTGNDC 87
           +D + KVTG ARYT D    G    K +RSP AH   + ++  +A  LPGV  I T  D 
Sbjct: 3   VDAIAKVTGRARYTDDYVMAGMCYAKYVRSPIAHGYAVSINDEQARSLPGVLAIFTWEDV 62

Query: 88  -DTPYGVIPIAQN---------EFPLARGRIRYVGEPVAAVAAVDEATTDAALALIRLKV 137
            D P+     A           +  L    +R+ G+ VA V A DE T + A  L+ ++ 
Sbjct: 63  PDIPFATAGHAWTLDENKRDTADRALLTRHVRHHGDAVAIVVARDELTAEKAAQLVSIEW 122

Query: 138 RELPAYFDAADARKADVVLLHDNKKGNIEREVHNEFGDAAAGFAAADLICEETFECAEVH 197
           +ELP       A   D   +H+   GN+ ++     G+      AAD   +  ++   + 
Sbjct: 123 QELPVITTPEAALAEDAAPIHNG--GNLLKQSTMSTGNVQQTIDAADYQVQGHYQTPVIQ 180

Query: 198 HAMMEPNASLAAWDNERGHLTLWSVTQVPYYVHESLARCMKLDAAYIRVIKPFVGGGFGH 257
           H  ME   SLA W  +   +T+ S TQ+P+ V   + + + +  + +RVIKPFVGGGFG+
Sbjct: 181 HCHMESVTSLA-WMEDDSRITIVSSTQIPHIVRRVVGQALDIPWSCVRVIKPFVGGGFGN 239

Query: 258 RVETLNFEIIAGLLARAARGTVRLLQTREEAFLTHRGRPQTYVRMKLGLTRDGRMTACEA 317
           + + L   + A L ++     V++  +REE FL  R R    +  ++G+ RDG +     
Sbjct: 240 KQDVLEEPMAAFLTSKLGGIPVKVSLSREECFLATRTRHAFTIDGQMGVNRDGTLKGYSL 299

Query: 318 EVVQRGGAYGGYGLVTILYAGALLNGLYDLPAVKYDGYRVYTNTPPCGAMRGHGTVNIRF 377
           +V+   GAY  +G       G  +  LY   A  Y     YTN P  GAMRG+G   + F
Sbjct: 300 DVLSNTGAYASHGHSIASAGGNKVAYLYPRCAYAYSSKTCYTNLPSAGAMRGYGAPQVVF 359

Query: 378 AFESLLDMMAAELGLDAFAVRRRNLLK-APTETINGLKVMSYGLPECLDWVEQASGWRER 436
           A ES+LD  A  LG+D   +R RN  +      + G ++ S GLPECL+   +   W +R
Sbjct: 360 AVESMLDDAATALGIDPVEIRLRNAAREGDANPLTGKRIYSAGLPECLEKGRKIFEWEKR 419

Query: 437 AARLEANSDGPIRRGIGIACSHFVSGSAKPVHFTGQPHATIALRVDFDAGITILTGASDI 496
            A  + N  G +RRG+G+AC  + S +  PV   G   A   L ++ D  I + +GA++I
Sbjct: 420 RAECQ-NQQGNLRRGVGVACFSYTS-NTWPV---GVEIAGARLLMNQDGTINVQSGATEI 474

Query: 497 GQGSSTIITQVVAEILGVEYRRLRLIAT-DSALTPKDNGSYSSRVTFMVGNAAADAARNL 555
           GQG+ T+ +Q+VAE +GV    +R+I+T D+ +TP D G+++SR +++   A   AA  L
Sbjct: 475 GQGADTVFSQMVAETVGVPVSDVRVISTQDTDVTPFDPGAFASRQSYVAAPALRSAALLL 534

Query: 556 KAVLVAAAAKRLQVAEADVDWLGEAAAVVGDASRQIPFHDIVEEALVDVGMLTVKGTFTC 615
           K  ++A AA  L  +  ++  +     +V          +  EE L+ +  L +   +  
Sbjct: 535 KEKIIAHAAVMLHQSAMNLTLIKGHIVLV----------ERPEEPLMSLKDLAMDAFY-- 582

Query: 616 PPEFQGGKQRGGAVGSTMG-FSYAAQAVEVSVDTELGKVTVEKVWSAIDCGFAINPMSVE 674
            PE  G      ++ +T    ++    V+++VD  L KVT+ ++ +  D G  +NP+  E
Sbjct: 583 HPERGGQLSAESSIKTTTNPPAFGCTFVDLTVDIALCKVTINRILNVHDSGHILNPLLAE 642

Query: 675 GQVQGAIWMGMGQAISEETVYE--NGRHKAVSLLDYRVPTIIESPDIAVHIVESLDPNGP 732
           GQV G + MG+G A+ EE + +  +G  +  +LLDY++PT+ + P +    VE  +P   
Sbjct: 643 GQVHGGMGMGIGWALFEEMIIDAKSGVVRNPNLLDYKMPTMPDLPQLESAFVEINEPQSA 702

Query: 733 FGAKEASEGPLAGVMSAIAAAIEDATGTRIRATPFTPDRVFD 774
           +G K   E P+  V +AI  A++ ATG  I   P TP R+++
Sbjct: 703 YGHKSLGEPPIIPVAAAIRNAVKMATGVAINTLPLTPKRLYE 744


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: 1271
Number of extensions: 59
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: 794
Length of database: 752
Length adjustment: 41
Effective length of query: 753
Effective length of database: 711
Effective search space:   535383
Effective search space used:   535383
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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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