Alignments for a candidate for hcrA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Cupriavidus basilensis 4G11

Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate RR42_RS13630 RR42_RS13630 4-hydroxybenzoyl-CoA reductase

Query= SwissProt::O33819
         (769 letters)



>FitnessBrowser__Cup4G11:RR42_RS13630
          Length = 764

 Score =  447 bits (1151), Expect = e-130
 Identities = 285/760 (37%), Positives = 410/760 (53%), Gaps = 18/760 (2%)

Query: 10  TVGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEGVI 69
           TVG  TP V   EKV G+A Y  DI     L  ++LRSP+ HARI+ IDT+AA AL GV 
Sbjct: 5   TVGSATPQVTAREKVMGRAVYAGDIKQAGMLHAKVLRSPYPHARIVRIDTAAARALRGVK 64

Query: 70  AVCTGAETPVPFGVLPIAENEYPLARDKVRYRGDPVAAVAAIDEVTAEKALALIKVDYEV 129
            V TG +TP         E    LA   VR+ G+ VAAV A+DE TA  AL LI+V+YE 
Sbjct: 65  LVLTGEDTPSRLWGTHRKEQRI-LAAGVVRHVGEEVAAVVAVDEETARDALDLIRVEYEE 123

Query: 130 LPAYMTPKAAMKAGAIALHDDKPNNILREVHAEFGDVAAAFAEADLIREKTYTFAEVNHV 189
           LPA  +P AA+  GA  LH     NI  E+H E GDV A FA A ++ E TY        
Sbjct: 124 LPAIFSPDAALADGAAELHPGT-RNIAHEMHIERGDVEAGFARAAVVYEATYDMHSQYPG 182

Query: 190 HMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIKPFLGGGFGART 249
           ++E  AT+A  D     LT+  +TQ  +    ++A  L    + IRVI+   GGGFGA+ 
Sbjct: 183 YLEPMATVAAQDG-NGRLTVWASTQSVFLARARLAEALDRPVSTIRVIQAVTGGGFGAKI 241

Query: 250 EGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTEVKMKIGLKKDGKIAALALEA 309
                 +IA LLA +    VRL+  R E F+  R      V +K+GL   G I A  +  
Sbjct: 242 VEESNSLIAALLATRLDRPVRLVNNRLEDFLGARSSVPARVWLKMGLDAQGMIVAKDVNI 301

Query: 310 TQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMRGHGTVDTRAAF 369
               GAYAG     +  T      ++ +  ++ +A   YTN PP GA RG G    +   
Sbjct: 302 VAECGAYAGLAGDVMHVTAMRSDNMHRVENVRSNAVLAYTNNPPRGAFRGFGGQQMQFPL 361

Query: 370 EALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRVMSYGVPECLEKVKAASGWEERKG 429
            + LT + E LG+D +++ + N + +    +++  ++ S G+ ECLE+ + A  W+ R+ 
Sbjct: 362 NSHLTMLAEMLGMDPIEVHKRNAI-RSGDTSVHGWKIGSSGLVECLEQTREAIQWDARRA 420

Query: 430 KLPKG-----RGLGIALSHFVSGTSTPKHWTGEPHATVNLKLDFDGGITLLTGAADIGQG 484
              +      RGLGIA +  VSG  T  +W G   +T+ LK++ DG + LLT   D+GQG
Sbjct: 421 DASRRTGTRRRGLGIAAAMHVSGNRTLGNWDG---STIVLKVNEDGRVMLLTSECDMGQG 477

Query: 485 SNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRVTFMVGNASISAAEELKGVL 544
           +NTM SQ+ A+ LG+ LS + V + D+ + P   GS +SRVT + GNA + AA E K  L
Sbjct: 478 ANTMLSQICAQELGIALSHVTVSAPDTDVAPFCLGSLASRVTIISGNAVMRAAREAKQKL 537

Query: 545 VKAAAKKLDAREEDIEVIDEMFMVSGSQDPGLSFQEVVKAAMVDSGT--ITVKGTYTCPT 602
           +  AA KL   ++++++ID +           +  E+ +  +   G   + V+ TY  PT
Sbjct: 538 LAVAAGKLGVPQDELDLIDGVIRARHDDTTRATLAEIARLHIFRHGGEGLMVRATYDAPT 597

Query: 603 EFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITGKVTAHKVWVAVDVGKALNPLAVEGQ 662
               D    G+   A   + +AAQ VE  VD +TG++T    +V+ D GKA+NPLAV GQ
Sbjct: 598 VMH-DANYYGNIAPA---YSFAAQAVEVEVDTVTGQITLIDSFVSDDCGKAINPLAVHGQ 653

Query: 663 TQGGVWMGMGQALSEETVYDNGRMVHGNILDYRVPTIVESPDIEVIIVESMDPNGPFGAK 722
           T G     +G  L E    ++GR+++GN  DY +PT    P +   +VES++PNGP+GAK
Sbjct: 654 THGATVQAIGWTLYEHVQVEDGRILNGNFADYTMPTADAVPALRTDVVESVEPNGPYGAK 713

Query: 723 EASEGMLAGFLPAIHEAVYEAVGVRATDFPLSPDRITELL 762
            ASE  +     AI  AVY+A+GVR    P++P+++   L
Sbjct: 714 GASETAILPGAAAIANAVYDAIGVRIASLPITPEKVLAAL 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: 1259
Number of extensions: 52
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: 764
Length adjustment: 41
Effective length of query: 728
Effective length of database: 723
Effective search space:   526344
Effective search space used:   526344
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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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