Alignments for a candidate for hcrA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Paraburkholderia bryophila 376MFSha3.1

Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate H281DRAFT_02676 H281DRAFT_02676 xanthine dehydrogenase, molybdenum binding subunit apoprotein (EC 1.17.1.4)

Query= SwissProt::O33819
         (769 letters)



>FitnessBrowser__Burk376:H281DRAFT_02676
          Length = 788

 Score =  309 bits (792), Expect = 3e-88
 Identities = 235/789 (29%), Positives = 375/789 (47%), Gaps = 49/789 (6%)

Query: 11  VGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEGVIA 70
           +G R    +  + + G+  Y  D+  P+ L   +LRS HAHA+I++ID +AA  L+GV A
Sbjct: 16  IGKRVTRTEDKKLLQGQGSYVDDVHLPNMLQAAVLRSSHAHAKIVSIDCTAARELKGVHA 75

Query: 71  VCTGAE----------TPVPFGVLPIAENEYPLARDKVRYRGDPVAAVAAIDEVTAEKAL 120
           V T A+          + +P   +     +  LA  +V + G+ VA V A +   AE A 
Sbjct: 76  VYTHADLSGRARGRAPSMLPNPAIRFERTQELLASTEVTFAGEAVAFVVADNRYIAEDAC 135

Query: 121 ALIKVDYEVLPAYMTPKAAMKAGAIALHDDKPNNILREVHAEFGDVAAAFAEADLIREKT 180
            LI+V+Y+ LPA    +  ++  +   H D  +N++  +   FGD+ AAF  A  + E+T
Sbjct: 136 GLIEVEYDTLPAVADCRDGLRPESPLCHTDAKDNVVAHIEMGFGDIDAAFNGAPHVVEET 195

Query: 181 YTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIKPF 240
           Y     +   ME    LAE+      LT+ ++ Q P++    +   L+ D+ ++RV+   
Sbjct: 196 YWQNRGSAHPMETRGYLAEFHAANGELTVWSSGQAPHHEKKNLVELLEWDAEKLRVLMND 255

Query: 241 LGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIA---HRGRPWTEVKMKIGLK 297
           +GGGFG +      E +  + A   K  V+ ++ R E F+A    R + WT   +KI L+
Sbjct: 256 VGGGFGPKLPFYPEEALVAIAAVALKRPVKWIEDRREHFLAVTQERDQWWT---VKIALE 312

Query: 298 KDGKIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAM 357
            DGKI  + LE     GA+  +GIIT   +     G Y IPA+      VYTN      +
Sbjct: 313 NDGKIRGVKLEMVHDNGAFLPWGIITPYISITTTPGPYVIPAMGAKLDVVYTNKCATSPV 372

Query: 358 RGHGTVDTRAAFEALLTEMGEELGIDSLKIRQINML--PQIPYVTMYAQ------RVMSY 409
           RG G      A E +L +    LG+D  ++R  N++   Q+PY   +        R  S 
Sbjct: 373 RGAGRPQAVFAMERILDKAARALGMDRAELRWRNLIQPEQMPYDAGFIYRDGSPLRYDSG 432

Query: 410 GVPEC----LEKVKAASGWEERKGKLPKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLK 465
             P C    LE+ K +S  + +     +GR +GI ++ FV GT         P     ++
Sbjct: 433 DYPACQKAALERAKYSSFAQRKAEARREGRFIGIGMASFVEGTGM------GPFEGATVR 486

Query: 466 LDFDGGITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRV 525
           +  +G I ++TGA+  GQG  T  +Q+ AE L V L  I VI+ D+       G+++SRV
Sbjct: 487 VQANGRIAVITGASPQGQGHKTTFAQICAEQLNVPLETIDVITGDTGGISMGVGTFASRV 546

Query: 526 TFMVGNASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQDPGLSFQEVVKAA 585
           T   GN+   AA+ +   ++   A     + E++ +++         +  +S+ ++ K +
Sbjct: 547 TVNAGNSVYIAAQAVGEKMLTLTAHLWKCKPEELLLVEGHVARRAGIEQRMSYGQLAKIS 606

Query: 586 MVDSGTITVKGTYTCPTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITGKVTAHKVW 645
               G       +T P       +       A   +C    VVE  VD  TG +T     
Sbjct: 607 QGMPG-------FTMPEGLTAGLEETKYFSPAQSTYCNGTAVVELEVDRETGHITILNYV 659

Query: 646 VAVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVYD-NGRMVHGNILDYRVPTIVESPD 704
           +A D GK +NP+ V+GQ  G V  G+G A  E   YD N + +  N  +Y +P   + P+
Sbjct: 660 MAHDSGKLINPMIVDGQVIGSVAHGIGNATLEWMQYDENAQPITTNFGEYLLPMATDVPN 719

Query: 705 IEVIIVESMDPNGPFGAKEASEG----MLAGFLPAIHEAVYEAVGVRATDFPLSPDRITE 760
           I+++ +E+  P  P G K A EG      A  + AI +A+ E  GV  T+ PL P R+ +
Sbjct: 720 IDIVHLETPSPLNPLGVKGAGEGGTIPAAAAIVAAIEDALSE-YGVEFTEAPLVPQRVFQ 778

Query: 761 LLDAKEAAA 769
            L  KEA A
Sbjct: 779 KL--KEAGA 785


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: 1346
Number of extensions: 74
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: 788
Length adjustment: 41
Effective length of query: 728
Effective length of database: 747
Effective search space:   543816
Effective search space used:   543816
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