Alignments for a candidate for ofo in Burkholderia vietnamiensis G4

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Burkholderia vietnamiensis G4

Align branched-chain ketoacid ferredoxin reductase (EC 1.2.7.7) active on 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate, or 3-methyl-2-oxobutanoate (characterized)
to candidate WP_011886186.1 MFS transporter

Query= reanno::psRCH2:GFF3452
         (1156 letters)



>NCBI__GCF_000016205.1:WP_011886186.1
          Length = 1198

 Score = 1077 bits (2784), Expect = 0.0
 Identities = 576/1163 (49%), Positives = 754/1163 (64%), Gaps = 32/1163 (2%)

Query: 2    SLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLD 61
            +L++ RL D      G ++LTGTQAL RL ++Q   D A+GLNT GF+SGYRGSPLG +D
Sbjct: 12   ALSDYRLTDNLTATRGRIFLTGTQALVRLLLMQRAADTAQGLNTAGFVSGYRGSPLGMVD 71

Query: 62   KSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDR 121
            + LW+A+  L    + F P +NEEL  TAV G+Q+    P    DGV+AMWYGKGPGVDR
Sbjct: 72   QQLWKAKKLLDAGGVRFLPAINEELGGTAVLGTQRVEADPERTVDGVYAMWYGKGPGVDR 131

Query: 122  AGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILD 181
            AGD  KH NA G SP GGVL++AGDDHGC SS++PHQS+ A +A  +P++NP+N+ ++L+
Sbjct: 132  AGDALKHGNAYGSSPHGGVLVVAGDDHGCVSSSMPHQSDFAMMAWHMPIVNPSNIADMLE 191

Query: 182  YGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD- 240
            +G+ GW LSRYSG WV  K I+E V+S + V++D L+ Q   P  F  P  G+H RWPD 
Sbjct: 192  FGLYGWALSRYSGAWVGFKAISETVESGSTVDLDALQTQWPAPAGFAPPAGGLHNRWPDL 251

Query: 241  PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300
            P L  E RL   K+ A R FARAN++++ +    +  +GI+T GK++LD+ +AL  L L 
Sbjct: 252  PSLTIEARL-AAKLDAVRHFARANSIDKWIAPGAHANVGIVTCGKAHLDLMEALRRLDLT 310

Query: 301  EALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSK 360
                 + G+R+ KVG+S+PLE   +  F  GL E+LV+EEK  +IE Q+   LYN     
Sbjct: 311  VGDLDAAGVRIYKVGLSYPLEMTRIDTFVDGLAEVLVIEEKGPVIEQQIKDYLYNRADGA 370

Query: 361  RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAA 420
            RPRV+G+ D  G  LL  L EL P+ I  V A  LA    +   + R+  L A +  L+ 
Sbjct: 371  RPRVLGKHDAAGACLLSELGELRPSRILPVFADWLARHKPTLDRRERVVDLVAPQ-ILSN 429

Query: 421  RSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWI 480
             + +  RTP++CSGCPHN+STKVPEGS A AGIGCH+M  WM+R T    QMGGEGV+W 
Sbjct: 430  EADAVKRTPYFCSGCPHNTSTKVPEGSIAQAGIGCHFMASWMERDTTGLIQMGGEGVDWA 489

Query: 481  GQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGEL 540
              A FT+T H+FQNLGDGTYFHSG LA+R AVAA  N+TYKILYNDAVAMTGGQP+DG +
Sbjct: 490  AHAMFTNTKHVFQNLGDGTYFHSGILAIRQAVAAKANITYKILYNDAVAMTGGQPVDGSI 549

Query: 541  RVDQLSRQIFHEGVKRIALVSDEPDKYPS-RDTFAPITSFHHRRELDAVQRELREFKGVS 599
             V Q++RQ+  EGV R  +VSDEP KY      F   T+FHHR ELDAVQRELRE  GV+
Sbjct: 550  SVPQIARQVEAEGVSRFVVVSDEPQKYDGHHGQFPAGTTFHHRSELDAVQRELRETPGVT 609

Query: 600  VIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRK 659
            V+IYDQTCA EKRRRRK+G+  DP KR FIN AVCEGCGDCG +SNCL+V PLET LGRK
Sbjct: 610  VLIYDQTCAAEKRRRRKKGEFPDPDKRLFINDAVCEGCGDCGVQSNCLSVEPLETPLGRK 669

Query: 660  REIDQNACNKDFSCVEGFCPSFVTVHGGGLRK-------PEAVAGGIEAATLPEPQHPTL 712
            R IDQ++CNKD+SCV GFCPSFVTV G  L+K         A+A  ++A  LP P     
Sbjct: 670  RRIDQSSCNKDYSCVNGFCPSFVTVEGAALKKAAGAAFDEAALAARVDA--LPVPATHLD 727

Query: 713  DRPWNVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQS 772
              P+++L+ GVGG+GV T+GAL+ MAAHLEGK  +VLD  G AQK G V + VRIA+   
Sbjct: 728  AAPYDMLVTGVGGTGVVTVGALISMAAHLEGKSASVLDFMGFAQKGGSVLSFVRIASSDR 787

Query: 773  DIYAVRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVP 832
             +  VRI   +AD+LL CD++V A  E+L  +  + +  VVN+H    A F +NPDA + 
Sbjct: 788  WLNQVRIDTQQADVLLACDMVVGASAEALQTVRHERTRIVVNTHRIPNASFVQNPDANLH 847

Query: 833  GAAMRQAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKA 892
              A+ + +  A GA      DA  LA + LGDSI  N+ +LG+A+Q GL+P+S  A+ +A
Sbjct: 848  ADALLEKMRHAAGAGHLSSCDAQALAAKFLGDSIGANILMLGYAWQLGLVPVSLAAMMRA 907

Query: 893  IELNGVSAKLNLQAFRWGRRAVLEREAVEQL-----------ARPVDMVEPICKTLEEIV 941
            IELN V+  +N  AF  GR A  +   ++ L           A   D ++P    L+ ++
Sbjct: 908  IELNNVAVPMNKLAFSIGRMAAGDATGLDALWRARHAGLAPMAGASDTLDPPA-PLDALI 966

Query: 942  DWRVDFLTRYQSAGLARRYRQLVERVRDADSADDLALSKAVARYYFKLLAYKDEYEVARL 1001
              R   L  Y  A    RYR LV   R   +  D AL++AVA  +++LLA KDEYEVARL
Sbjct: 967  ADRETRLAAYGGARYVARYRALVNAAR---AKGDEALTRAVATTFYRLLAVKDEYEVARL 1023

Query: 1002 YSEPEFRQQLEAQFEG----DYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLA 1057
            Y++  FR  LEAQFEG    DY+++F+LAP  LAK       P+KR  G W+  + GVLA
Sbjct: 1024 YADGAFRAALEAQFEGAPGQDYRVKFNLAPPALAKAGRDGSAPQKRVFGQWLWPVLGVLA 1083

Query: 1058 KFRFLRGTPLDPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRG 1117
            + R LRGTPLDPFG   +RR+ER L  +YE T+   LA +   N      +A L  ++RG
Sbjct: 1084 RVRSLRGTPLDPFGRTAERRMERALADDYETTLTRALAAMTAANAAQVAQLAELHARVRG 1143

Query: 1118 YGPVKERSIAKARQQEKLLREQL 1140
            +G VK R++A  ++ E+ L  QL
Sbjct: 1144 FGHVKVRNLAGVKRAERELALQL 1166


Lambda     K      H
   0.319    0.136    0.405 

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: 3096
Number of extensions: 126
Number of successful extensions: 7
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: 1156
Length of database: 1198
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1151
Effective search space:  1276459
Effective search space used:  1276459
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: 58 (26.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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