Aligments for a candidate for hcrA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for hcrA in Phaeobacter inhibens BS107

Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate GFF1600 PGA1_c16220 molybdopterin binding domain-containing protein

Query= SwissProt::O33819
         (769 letters)



>FitnessBrowser__Phaeo:GFF1600
          Length = 756

 Score =  333 bits (855), Expect = 2e-95
 Identities = 266/778 (34%), Positives = 378/778 (48%), Gaps = 58/778 (7%)

Query: 11  VGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEGVIA 70
           VG R    DG++KVTGKA++ AD  AP  L G ILRSPHAHARI  IDTS AEAL  V A
Sbjct: 13  VGTRPNRPDGLDKVTGKARFGADATAPGMLFGAILRSPHAHARIKQIDTSKAEALADVKA 72

Query: 71  VCTGAETPVPFGVLPIAENEY------PLARDKVRYRGDPVAAVAAIDEVTAEKALALIK 124
           + T A+        P  E E        +A D   Y G  +AAVAA   + A  AL LI+
Sbjct: 73  IVTRADFSDAIKPAPGLEGEQWNVLENVMAGDTALYDGHAIAAVAATSALAARDALKLIE 132

Query: 125 VDYEVLPAYMTPKAAMKAGAIALHDDKPN---------NILREVHAEFGDVAAAFAEADL 175
           V+YEVLP       AM   A  + +   +         N++R   +  GDV A FA+ADL
Sbjct: 133 VEYEVLPHVTDVDKAMAQDAPVIREGAADYSVPEGMHPNVVRYHESGHGDVEAGFAKADL 192

Query: 176 IREKTYTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIR 235
           + E+ +     +  ++E +A LA+         L   TQ  +YV    AA L ++++++R
Sbjct: 193 VVEEHFVTEATHQGYIEPHACLAQLGQ-DGKGELWCCTQGHWYVQKNCAALLGIETSQLR 251

Query: 236 VIKPFLGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTEVKMKIG 295
           V    +GGGFG +T  +  E +A  L+RK+   V+L+ +R E F A      T + +KIG
Sbjct: 252 VTASEIGGGFGGKTT-VFIEPVALALSRKSNRPVKLVMSRPEVFRATGPTASTSMDIKIG 310

Query: 296 LKKDGKIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCG 355
           +  DG I A        GGA+ G             + L H+  + +D   + +N P   
Sbjct: 311 MTADGIITAAQGTFRLQGGAFPGAPADMTAMCAFAPYDLQHVQQVGYD---IMSNRPKQA 367

Query: 356 AMRGHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRVMSYGVPECL 415
           A R  G+     A E+++ E+  +L +D + +R  N   +    + Y  +    G+ E L
Sbjct: 368 AYRAPGSPMAAYAVESVIDELCRKLDLDPVDVRLKNAAREGTRAS-YGPKFERIGLVETL 426

Query: 416 EKVKAASGWEERKGKLPKGRGLGIALSH-FVSGTSTPKHWTGEPHATVNLKLDFDGGITL 474
           +  KA   +      L  G+G GI+    F  G  T          +V+L L  DG   +
Sbjct: 427 DAAKAHPHY---SAPLKSGQGRGISCGFWFNHGGET----------SVSLSLSEDGTCQI 473

Query: 475 LTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRVTFMVGNASI 534
             G  DIG GS    + +AAEVLG+    IRV  AD+A    ++ S+ SRVT+  G A+I
Sbjct: 474 SVGTPDIG-GSRASMALMAAEVLGIPYESIRVTIADTATLGYNDVSHGSRVTYASGLATI 532

Query: 535 SAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQ----DPGLSFQEVVKAAMVDSG 590
            AAE+    L K AA K    E+ ++  D   + SG      DP L   E+ +      G
Sbjct: 533 KAAEDAVAKLSKRAAAKWGIPEDAVKWEDGHAVPSGPNAGNFDP-LPLAEITRDMGQTGG 591

Query: 591 TITVKGTYTCPTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITGKVTAHKVWVAVDV 650
            I+  G +    E            GA  G  +A  +V+A VD  TGK    +  V  D 
Sbjct: 592 PIS--GHFEATPE------------GA--GVSFATHIVDAEVDPETGKTAVTRYTVIQDA 635

Query: 651 GKALNPLAVEGQTQGGVWMGMGQALSEETVY-DNGRMVHGNILDYRVPTIVESPDIEVII 709
           GKA++P  VEGQ QGG   G+G AL+EE +Y ++GR+ +   LDYR+P   + P I+ +I
Sbjct: 636 GKAIHPTYVEGQFQGGAAQGIGWALNEEYIYGEDGRLQNAVFLDYRIPVASDLPMIDTVI 695

Query: 710 VESMDPNGPFGAKEASEGMLAGFLPAIHEAVYEAVGVRATDFPLSPDRITELLDAKEA 767
           VE  +P  PFG +   E  +   L AI  AV  A GVR    P+SP RI   LD + A
Sbjct: 696 VEVPNPGHPFGVRGVGETSICPPLAAIANAVSAAAGVRLHALPMSPPRILAALDQQRA 753


Lambda     K      H
   0.317    0.134    0.386 

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: 1266
Number of extensions: 61
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: 769
Length of database: 756
Length adjustment: 40
Effective length of query: 729
Effective length of database: 716
Effective search space:   521964
Effective search space used:   521964
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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)
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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, or view the source code.

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