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 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_011882983.1 MFS transporter

Query= reanno::Cup4G11:RR42_RS19540
         (1197 letters)



>NCBI__GCF_000016205.1:WP_011882983.1
          Length = 1196

 Score = 1806 bits (4677), Expect = 0.0
 Identities = 893/1196 (74%), Positives = 1002/1196 (83%), Gaps = 8/1196 (0%)

Query: 1    MNAPLTPPVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTA 60
            MNAPL      ++  AL +V+L+DKYTLERGR Y+SG QALVRLPMLQ+ERDRAAGLNTA
Sbjct: 1    MNAPLDAGQRASLEAALKSVTLDDKYTLERGRAYMSGIQALVRLPMLQQERDRAAGLNTA 60

Query: 61   GFISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFE 120
            GFISGYRGSPLG LD SLWKAKQHLAAH IVFQ GLNEDLAAT+VWGSQQVN+YP A+++
Sbjct: 61   GFISGYRGSPLGGLDLSLWKAKQHLAAHQIVFQPGLNEDLAATAVWGSQQVNLYPGAKYD 120

Query: 121  GVFGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKAC 180
            GVFGMWYGKGPGVDRT DVFKHANSAGSS HGGVLVLAGDDHAAKSSTLAHQSEHIFKAC
Sbjct: 121  GVFGMWYGKGPGVDRTGDVFKHANSAGSSAHGGVLVLAGDDHAAKSSTLAHQSEHIFKAC 180

Query: 181  GLPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQD 240
            GLPVL+PSNVQEYLD+GLH WAMSRYSGLWV++KCVTDVVESSASV++DPHR +IVLP D
Sbjct: 181  GLPVLFPSNVQEYLDFGLHGWAMSRYSGLWVALKCVTDVVESSASVDIDPHRTDIVLPTD 240

Query: 241  FILPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKA 300
            F+LP GGLNIRWPDPPL QEARLLDYKWYA LAYVRANK+DRIEIDSP+ARFGIMT GKA
Sbjct: 241  FVLPEGGLNIRWPDPPLVQEARLLDYKWYAALAYVRANKLDRIEIDSPNARFGIMTAGKA 300

Query: 301  YLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIME 360
            +LD RQAL +LGLDD+TCARIGIRLYKVGCVWPLEA GA+AFA GL EILVVEEKRQI+E
Sbjct: 301  HLDVRQALTDLGLDDDTCARIGIRLYKVGCVWPLEAQGAQAFARGLDEILVVEEKRQILE 360

Query: 361  YALKEELYNWRDDVRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRL 420
            YA+KEELYNW D  RP+V+GKFDEKD AGGEWS+P  NWLLPAHYELSPAIIA+AIATRL
Sbjct: 361  YAIKEELYNWPDAQRPRVFGKFDEKDGAGGEWSVPMGNWLLPAHYELSPAIIAKAIATRL 420

Query: 421  DKFELPADVRARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALA 480
            DKFELP+DVRARIAAR+AVI AKE A+A P V  ERKPWFCSGCPHNTSTNVPEGSRA+A
Sbjct: 421  DKFELPSDVRARIAARLAVINAKEMALAKPHVQTERKPWFCSGCPHNTSTNVPEGSRAIA 480

Query: 481  GIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRAS 540
            GIGCHYMTVWMDR+TSTFSQMGGEGV WIGQAPF  +KHVFANLGDGTYFHSGLLA+RA+
Sbjct: 481  GIGCHYMTVWMDRNTSTFSQMGGEGVPWIGQAPFTDEKHVFANLGDGTYFHSGLLAVRAA 540

Query: 541  IAAGVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKY-SAA 599
            I++  NITYKILYNDAVAMTGGQP+DG L+V  + +Q+A+EGA++IV+VTDEPEKY S  
Sbjct: 541  ISSKANITYKILYNDAVAMTGGQPVDGVLTVPQITHQLASEGAKRIVIVTDEPEKYDSQK 600

Query: 600  IKLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFIN 659
              L  GV VHHRD+LD +QRELRE+ G TILIYDQTCATEKRRRRKRGTYPDPAKR  IN
Sbjct: 601  ALLAPGVTVHHRDQLDDVQRELREIAGTTILIYDQTCATEKRRRRKRGTYPDPAKRVVIN 660

Query: 660  DAVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVK 719
            DAVCEGCGDCSVKSNCLSVEPLETE GTKRQINQSSCNKDFSCV GFCPSFVT EG Q+K
Sbjct: 661  DAVCEGCGDCSVKSNCLSVEPLETEFGTKRQINQSSCNKDFSCVKGFCPSFVTVEGGQLK 720

Query: 720  KPERHGVSMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVL 779
            KP+   V    LP +P+PALP ++  YGVLVTGVGGTGVVTIG LLGMAAHLENKGVTVL
Sbjct: 721  KPKAVAVDGGALPPIPEPALPAIDRAYGVLVTGVGGTGVVTIGALLGMAAHLENKGVTVL 780

Query: 780  DMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRT 839
            D+ GLAQKGGAV+SHVQI+  P  +HATRIAMGEADLVIGCDAIV+A D+  S+ +   T
Sbjct: 781  DVTGLAQKGGAVMSHVQISHAPTDIHATRIAMGEADLVIGCDAIVTAGDECTSRMRRDAT 840

Query: 840  RAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVGEACDFINASGLAVALIGDAIFTNP 899
            R +VN+AQTPTAEFIKNP W FPGLSAE D+R A GEA DFI+A+  AVAL+GDAI+TNP
Sbjct: 841  RVVVNSAQTPTAEFIKNPNWTFPGLSAENDIRAAAGEAVDFIDANRFAVALLGDAIYTNP 900

Query: 900  LVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNT 959
             VLGYAWQKGWLPL+L +L RAIELN  +VEKN+AAFDWGR  AHD   V          
Sbjct: 901  FVLGYAWQKGWLPLTLASLERAIELNAVSVEKNRAAFDWGRRAAHDLASVKQAAAGAAGA 960

Query: 960  AEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALV-GNGK 1018
            A+ A V+ L T     ++ LIA R E LTAYQ+AAYA  +   V +VRAAE AL  G+  
Sbjct: 961  AQRATVIALHTKKA--VDALIAKRVEFLTAYQNAAYAARYAAFVDKVRAAERALADGDAA 1018

Query: 1019 PLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLM 1078
              PLTEA ARNL KLMAYKDEYEVARL +DP F+ +L +QFEG    D++L F LAPPL 
Sbjct: 1019 QEPLTEAVARNLFKLMAYKDEYEVARLQSDPAFVARLSSQFEG----DWKLKFHLAPPLF 1074

Query: 1079 AKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLE 1138
            AK+D  GHLVK+ +GP  +  F +LAK K LRG   D FG+T ERRTERALIGEY AL++
Sbjct: 1075 AKKDAHGHLVKKAYGPWMLSAFRLLAKAKFLRGTGLDPFGRTEERRTERALIGEYEALID 1134

Query: 1139 ELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPETAQ 1194
            E+   L AAN   A+ LA+LPD IRGFGHVK++NL  VR +W ALL ++R P   Q
Sbjct: 1135 EVLGRLDAANRPLALELAALPDGIRGFGHVKENNLRAVRQKWDALLAKWRSPAGGQ 1190


Lambda     K      H
   0.319    0.135    0.407 

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: 3642
Number of extensions: 143
Number of successful extensions: 5
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: 1197
Length of database: 1196
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1149
Effective search space:  1321350
Effective search space used:  1321350
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 (21.7 bits)
S2: 59 (27.3 bits)

This GapMind analysis is from Apr 09 2024. 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 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