GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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