Alignments for a candidate for hcrA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Dinoroseobacter shibae DFL-12

Align 4-hydroxybenzoyl-CoA reductase, α subunit (EC 1.3.7.9) (characterized)
to candidate 3607631 Dshi_1040 aldehyde oxidase and xanthine dehydrogenase molybdopterin binding (RefSeq)

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



>FitnessBrowser__Dino:3607631
          Length = 763

 Score =  243 bits (619), Expect = 4e-68
 Identities = 228/768 (29%), Positives = 321/768 (41%), Gaps = 55/768 (7%)

Query: 34  VTGTARYTADLPAQGALVGKLLRSPYAHAELLEVDISEALKLPGVRGIVTGNDCD----- 88
           V G   + AD+PA+GAL  +++RSPY    +  +D+  A  +PGV  +++G D       
Sbjct: 21  VRGAGCFVADVPAEGALWMEVVRSPYPAGRITALDLDAARAMPGVVCVLSGADQAGLRPF 80

Query: 89  ----TPYGVIPIAQNEFPLARGRIRYVGEPVAAVAAVDEATTDAALALIRLKVRELPAYF 144
                P G   +     P+A  R+ +VGEPVA V A        A   + L+V E P   
Sbjct: 81  PLRYVPKGCDVVPTPFLPMATDRVTWVGEPVAVVVAETAGQASDAADAVVLEVAEAPVVT 140

Query: 145 DAADARKADVVLLHDNKKGNIEREVHNEFGDAAAGFAAADLICEET---FECAEVHHAMM 201
           DA      +   +  ++  NI      E GD  A  AAA      T    E + V    +
Sbjct: 141 DARTGAAPEAPRVWPDRDSNIAFTY--ELGDRDAFEAAAARAAHVTRARIEISRVAAMTL 198

Query: 202 EPNASLAAWDNERGHLTLWSVTQVPYYVHESLARCMKLDAAYIRVIKPFVGGGFGHRVET 261
           EP  +LA    E GH+TLW+ TQ P+ V   LA  + L    IRV K   GG FG R   
Sbjct: 199 EPRGALATCSPE-GHMTLWTGTQAPHRVQGELAHVLDLPLDRIRVRKTDTGGSFGMRNGA 257

Query: 262 LNFEIIAGLLARAARGTVRLLQTREEAFLTHRGRPQTYVRMKLGLTRDGRMTACE----A 317
              + +A L ARA    V    TR E FL      +  V   L L  DG   A +    A
Sbjct: 258 FPEDALALLAARATGRPVHWQGTRSEGFLADTASREQSVDAALALDADGTFLALQVDGYA 317

Query: 318 EVVQRGGAYGGYGLVTILYAGALLNGLYDLPAVKYDGYRVYTNTPPCGAMRGHGTVNIRF 377
            +  + G   G+ + + L     L G+Y  P +      V+ N       RG G     +
Sbjct: 318 PIGAQMGQMSGHPMTSNLPG---LAGVYRTPVIHAVMRGVHVNAMHMAPYRGAGRPEAIY 374

Query: 378 AFESLLDMMAAELGLDAFAVRRRNLL---KAPTETINGLKVMSYGLPECLDWVEQASGWR 434
             E ++++ AAE G D  A+R RN++   + P  T +G    S   P  L      +   
Sbjct: 375 VIERMVELAAAETGRDPVALRLRNMIGPDQMPWATPHGFTYDSGDFPTALRAALAGADAA 434

Query: 435 ERAARLEANSDGPIRRGIGIACSHFVSGSAKPVHFTGQPHATIALRVDFDAGITILTGAS 494
             AAR EA       RG+GIAC+   +G        G      A  +    G+ I TGA 
Sbjct: 435 GFAARREAARARGRLRGLGIACAIEPAGGGP----KGAQLPEYAQLIAGPEGLEIRTGAG 490

Query: 495 DIGQGSSTIITQVVAEILGVEYRRLRLIATDSALTPKDNGSYSSRVTFMVGNAAADAARN 554
           D GQG +T   Q+   +LG     + +   D+    +  G++ SR    VG A    +  
Sbjct: 491 DAGQGHATAFAQIAERLLGWR-GPVTVRGGDTGEIARGTGTFGSRTMGSVGAAMQAGSAQ 549

Query: 555 LKAVLVAAAAKRLQVAEADVDWLGEAAAVVGDASRQIPFHDIVEEALVDVGMLTVKGTFT 614
           +       AA  L+VA  D+ +   A  V G   R IP  ++               TFT
Sbjct: 550 ILEAARPEAADLLEVAARDLVFAQGAFRVAG-TDRAIPLAEVTAR---------TGRTFT 599

Query: 615 CPPEFQGGKQRGGAVGSTMG-FSYAAQAVEVSVDTELGKVTVEKVWSAIDCGFAINPMSV 673
                         V +  G F   A   EV VD + G V +     A D G  INP+ V
Sbjct: 600 AE----------AFVATEAGTFPNGAHVAEVEVDPDTGAVQLAAYTVADDVGTVINPLLV 649

Query: 674 EGQVQGAIWMGMGQAISEETVYE-NGRHKAVSLLDYRVPTIIESPDIAVHIVESLDPNGP 732
           EGQV G +  G+GQA+ E  V++ +      SL+DY VP   +   I V    +     P
Sbjct: 650 EGQVHGGVAQGLGQALMERIVHDADAALLTGSLMDYAVPRATDLCRIEVLHTPTPTTANP 709

Query: 733 FGAKEASEGPLAGVMSAIAAAIEDATG---TRIRATPFTPDRVFDALN 777
            G K A E    G ++A+  A+ DA G    R    P +P RV+ ALN
Sbjct: 710 LGVKGAGESGTVGALAAVMNAVCDAIGPEAARRLQMPASPHRVWAALN 757


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: 1516
Number of extensions: 94
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: 794
Length of database: 763
Length adjustment: 41
Effective length of query: 753
Effective length of database: 722
Effective search space:   543666
Effective search space used:   543666
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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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