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 HbaC subunit (EC 1.3.7.9) (characterized)
to candidate 3610338 Dshi_3719 aldehyde oxidase and xanthine dehydrogenase molybdopterin binding (RefSeq)

Query= metacyc::MONOMER-17404
         (777 letters)



>FitnessBrowser__Dino:3610338
          Length = 983

 Score =  261 bits (666), Expect = 2e-73
 Identities = 243/796 (30%), Positives = 343/796 (43%), Gaps = 63/796 (7%)

Query: 18  VDGIDKVTGRARYTADLDHT-GALVARILRSPISHGDIVRLDVSKALALDGVAAIVTGED 76
           V+    +TGR ++  DL    G L A ILRSP +H  I  +    A  L GV A++TGED
Sbjct: 13  VEDAPLLTGRGQFFDDLPTPHGTLQAAILRSPYAHARITDISADAARRLAGVHAVLTGED 72

Query: 77  CAITYGVLPIAMNE----YPMARDRVRYRGEPVAAVAAVDAETARQALDLIELELRELPA 132
            A     L + +      +P+ARD+VRY GEPVA V A D   A  ALDLIE+    L  
Sbjct: 73  YASVASPLMVGVKLPIECWPIARDKVRYVGEPVAVVLADDRYLAEDALDLIEVSYDTLAP 132

Query: 133 YYESEAARAPDAWLLHDNKPGNIEREVHNEFGDLAAGFEAADLIRTHTHHCAEVNHAQIE 192
             +   A A DA +LHD   GN+  +    +GD  + F  AD +   +      +   IE
Sbjct: 133 VIDPLKALADDAPVLHDEMGGNLGADRRFSYGDPDSAFAEADHVVEISVRYPRNSCTPIE 192

Query: 193 PHACLMDYDPVTGRLTAQSVSQVGYYLHLMLARCLEIDPSRVRVIKP-FVGGGFGARVEV 251
            +  L  ++P T      S  Q  + +H ++AR L +  +R+R+  P   GG FG +  V
Sbjct: 193 TYGVLTRWNPHTRSYDVTSNFQGPFSIHPVVARALNVPGNRLRLRTPEDSGGSFGIKQGV 252

Query: 252 LNFEVIAALLARKASGRVLMRLSREETFITHRARPQTDITLTIGTRRDGRFTACSCEVVQ 311
             +  + +  AR A   V     R E      +     ITL       GR TA   + V+
Sbjct: 253 FPYIALLSACARLADRPVKWVEDRLEHLTASVSATNRAITLRAAVTAKGRVTALDYDQVE 312

Query: 312 RGGAYAGYGIVTILY-AGALLQGLYDIPAVKYDGYRVYTNLPPCGAMRGHGSVDVRHAFE 370
             GAY        LY     L G YDI  ++     V TN  P G  RG G   +  A E
Sbjct: 313 DVGAYLRAPEPATLYRMHGNLCGAYDIANLRVRNRIVMTNKTPTGLNRGFGGPQIYFALE 372

Query: 371 NLVDRMARELGLDPFAVRRANLL---AAPTRTLNDLMVNSYGLAECLDKVERASGW---- 423
            L+ R+A ELGLDP  V R NL+   A P RT +    +S       D   +   +    
Sbjct: 373 RLMQRIAIELGLDPVNVARDNLIPKGAFPYRTASGATYDSGDYQNAFDTALKDGRYDALC 432

Query: 424 HERIGRLPPGK--GLGMACS--------HYVSGSAKPIHFT-----GEPHAVVALRLDFD 468
            +R      G+  G+G+A +         Y+S +  P             +   + +D  
Sbjct: 433 QKRDAARAEGRLYGIGLAVAVEPSVSNMGYLSTALTPAERAKAGPKNGAQSCATIAIDPV 492

Query: 469 GGITALTGAADIGQGSSTVVAITVAETLGVALNRVRVISGDSAITPKD-----NGAYSSR 523
           G IT    +   GQG  TV A  VAE  G+    + V++  +  T KD      G YSSR
Sbjct: 493 GSITVQIDSVPQGQGHKTVAASIVAERFGLEPGAITVVA--AMDTGKDAWSIAAGNYSSR 550

Query: 524 ITFMVGNAAIDAATKLKQILIAAAARKLEAVPEQIECAGESFFIGSGAQAALGFAEVVK- 582
                  A   AA +L++ + A AA +L A PE IE      FI S   AAL FA V   
Sbjct: 551 FAAASAGAVRIAADRLRERIAAIAASQLNARPEDIEFENGKVFIASNPGAALVFARVAST 610

Query: 583 ------------AALVDEGAITVKGIFTCPPESQGGQHRGGAVGSTMGFSYAAQVVEVSV 630
                       AA + E AI      T P +  G       + S++  ++      V +
Sbjct: 611 GHWAPGTLPDGIAAPMRETAIWTAPELTAPTDEDG-------INSSLCHAFIFDFCGVEI 663

Query: 631 DDATGLITVDKVWAALDCGRAINPLAVVGQVQGAVWMGMGQAMCEETRY-LDGLPAHASF 689
           D  T    VD      DCG  ++   V GQ++GA    +G A+ EE  Y  DG     + 
Sbjct: 664 DPVTHEARVDHYVTMHDCGTILHEGMVEGQIRGAFAQAVGAALYEEYVYDDDGAFLAGTL 723

Query: 690 LEYRMPTMIESPPIEVAIVESVDPFGPFGAKEASEGALAGFPPAMVNAVANAI-----GI 744
            +Y +PT+ E P +E+    +  P  P GAK   EG     P  + NAVA+A+      +
Sbjct: 724 ADYPVPTVHEIPDLEILHTCTPSPLTPLGAKGVGEGNCMSTPVCIANAVADALAPARGNV 783

Query: 745 DLDDLPATPDRVVEAL 760
           D+  LP +P R+   L
Sbjct: 784 DV-TLPLSPARIASYL 798


Lambda     K      H
   0.320    0.136    0.402 

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: 1881
Number of extensions: 107
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: 777
Length of database: 983
Length adjustment: 42
Effective length of query: 735
Effective length of database: 941
Effective search space:   691635
Effective search space used:   691635
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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