Alignments for a candidate for hcrA in Nocardioides daejeonensis MJ31

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Nocardioides daejeonensis MJ31

Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate WP_110208202.1 DNK54_RS17005 xanthine dehydrogenase family protein molybdopterin-binding subunit

Query= SwissProt::O33819
         (769 letters)



>NCBI__GCF_003194585.1:WP_110208202.1
          Length = 786

 Score =  285 bits (729), Expect = 7e-81
 Identities = 237/794 (29%), Positives = 363/794 (45%), Gaps = 65/794 (8%)

Query: 11  VGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEGVIA 70
           +G     V+    + G+ ++ AD+  P  L  R++RSP AH RI +IDTSAA AL GV A
Sbjct: 2   IGESLQRVEDPVLLRGQGRFAADVTLPGQLHMRVVRSPVAHGRIRSIDTSAARALPGVAA 61

Query: 71  VCTGAET----PVPFGVLPIAENEYP-----LARDKVRYRGDPVAAVAAIDEVTAEKALA 121
           V T  +     P+ F + PI E+  P     LAR +VRY G+PVA V A  E  AE A  
Sbjct: 62  VWTHDDIADLPPIAFRLTPI-ESMLPYRQPVLARGRVRYVGEPVAVVFAESEYLAEDAAE 120

Query: 122 LIKVDYEVLPAYMTPKA--------------AMKAGAIALHDDKPNNILREVHAEFGDVA 167
           L+ V+ E LPA + P                A++A   A  D++   I    H E+GD  
Sbjct: 121 LVDVEVEALPATVDPTGEPTPWLDAEEVAWTAVEAADGAGRDNESATI----HLEYGDPD 176

Query: 168 AAFAEADLIREKTYTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACL 227
           AAFA A  + +        + V ME     A  D    +L +N   +VP++    +A  +
Sbjct: 177 AAFAAAAHVFDVDVRVGRHSGVPMECRGGSAHVDAATGVLMVNGAAKVPFWNRDAIAQMV 236

Query: 228 QMDSARIRVIKPFLGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPW 287
                 +++I+  +GGGFG R E    +++  L   +    VR ++ R+E          
Sbjct: 237 GRSPHEVQLIEGHVGGGFGPRGELYPEDVLVPLATIRLGRPVRWVEDRQEHLTTCNHSRD 296

Query: 288 TEVKMKIGLKKDGKIAALALEATQAGGAYAG-YGIITILYTGALMHGLYHIPAIKHDAWR 346
              +++  + + G I AL  E     GAY   +G      T +++ G Y +P+ +     
Sbjct: 297 QRHRLRAAVDETGLITALDGEFWADQGAYVRTHGATVAGLTASMLPGPYLLPSYRITGHV 356

Query: 347 VYTNTPPCGAMRGHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLP------QIPYVT 400
             +N  P G  R  G  +   A E L+  +   LG+D +++R+ N +P      + P + 
Sbjct: 357 RMSNKTPAGTYRSPGRYEGTFARERLIDAIANGLGLDRIELRRRNFIPADAMPYRRPILA 416

Query: 401 MYAQRVMSYGVPECL-----EKVKAASGWEERKGKLPKGRGLGIALSHFVSGTSTPKHWT 455
           M  + V   G    L     E     +  EE   +   G  +GI    FV  +       
Sbjct: 417 MGTELVYDSGDYALLMDRMEETFDLPTLREEVAARREAGELVGIGYGWFVEKSGLG---- 472

Query: 456 GEPHATVNLKLDFDGGITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTP 515
             P     + +D  G   + TGA+ +GQG +T+ SQV  EVL + L RIR +   +    
Sbjct: 473 --PSEGARVMVDTGGSALVTTGASSVGQGVDTVLSQVVGEVLDLDLDRIRTVRGQTEHFN 530

Query: 516 KDNGSYSSRVTFMVGNASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQDPG 575
              G++++R + MVGNA + +A  ++   ++ AA  L+  E D+E++     V G+   G
Sbjct: 531 YGRGAFATRQSVMVGNAVLESALAVRAKALRVAAHHLEIDEADLELVRGRVQVVGTPGTG 590

Query: 576 LSFQEVVKAAMVD---SGTITVKGTYTCPTEFQGDKKIRGSAIGATMGFCYAAQVVEASV 632
           L   E+  AA+++   +  I  +   TC   F  D           M + Y   V    +
Sbjct: 591 LGLGEI--AALLEPHRAKAIGEEPGLTCDGWFHSDH----------MTYPYGVHVAVVQI 638

Query: 633 DEITGKVTAHKVWVAVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVY-DNGRMVHGNI 691
           D  TGK T  +  V  DVGKALN L VEGQ  GG   G+G AL EE  Y ++G+      
Sbjct: 639 DRGTGKPTLERFLVGYDVGKALNHLLVEGQITGGAAQGIGGALYEEFRYAEDGQPQATTF 698

Query: 692 LDYRVPTIVESPDIEVIIVE-SMDPNGPFGAKEASEGMLAGFLPAIHEAVYEAVG--VRA 748
           +DY +PT+ E P+  V++ E +  P  P G K A EG       AI  AV +A+      
Sbjct: 699 MDYLMPTMAEMPEFGVLVTEDAPSPLNPLGVKGAGEGGTTATAAAIASAVDDALSRPGSV 758

Query: 749 TDFPLSPDRITELL 762
           T  P+ PD I +L+
Sbjct: 759 TQTPIRPDLIRQLI 772


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: 1362
Number of extensions: 75
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: 769
Length of database: 786
Length adjustment: 41
Effective length of query: 728
Effective length of database: 745
Effective search space:   542360
Effective search space used:   542360
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 24 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
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 2024 update 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