Alignments for a candidate for ofo in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Paraburkholderia phymatum STM815

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_012402219.1 BPHY_RS14615 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000020045.1:WP_012402219.1
          Length = 1200

 Score = 1796 bits (4651), Expect = 0.0
 Identities = 870/1198 (72%), Positives = 1010/1198 (84%), Gaps = 13/1198 (1%)

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

Query: 61   GFISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFE 120
            GFISGYRGSPLG LD SLWKAK+HLAAH +VFQ G+NEDLAAT+VWGSQQVN+YP A+++
Sbjct: 61   GFISGYRGSPLGGLDLSLWKAKKHLAAHQVVFQPGVNEDLAATAVWGSQQVNLYPSAKYD 120

Query: 121  GVFGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKAC 180
            GVF MWYGKGPGVDR+ DVFKH NSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEH+FKAC
Sbjct: 121  GVFSMWYGKGPGVDRSGDVFKHGNSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHLFKAC 180

Query: 181  GLPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQD 240
            GLPVL+PSNVQEYLD+GLH WAMSRYSGLWV+MKCVTDVVESSASV++DPHR +I+LP D
Sbjct: 181  GLPVLFPSNVQEYLDFGLHGWAMSRYSGLWVAMKCVTDVVESSASVDIDPHRTQIILPAD 240

Query: 241  FILPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKA 300
            F +P GGLNIRWPDPPL QEARLLDYKWYAGLAYVRANK+DR+EIDSPHARFGI+TGGKA
Sbjct: 241  FAMPEGGLNIRWPDPPLVQEARLLDYKWYAGLAYVRANKLDRVEIDSPHARFGIITGGKA 300

Query: 301  YLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIME 360
            YLD RQAL +LGLDDETC+RIGIRLYKVGCVWPLEA GA+AFA  LQEILVVEEKRQI+E
Sbjct: 301  YLDVRQALTDLGLDDETCSRIGIRLYKVGCVWPLEAQGAQAFARELQEILVVEEKRQILE 360

Query: 361  YALKEELYNWRDDVRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRL 420
            YA+KEELYNW D  RP+V+GKFDEKD AGGEWS+P  NWLLPAHYELSPA+IA+AIATRL
Sbjct: 361  YAIKEELYNWPDAQRPRVFGKFDEKDGAGGEWSVPMGNWLLPAHYELSPALIAKAIATRL 420

Query: 421  DKFELPADVRARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALA 480
            DKF+LP+DVRARIAARIAVIEAKEKA+A P+VA ERKPWFCSGCPHNTSTNVPEGSRA+A
Sbjct: 421  DKFDLPSDVRARIAARIAVIEAKEKALARPKVAIERKPWFCSGCPHNTSTNVPEGSRAMA 480

Query: 481  GIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRAS 540
            GIGCHYMTVWMDRSTSTFSQMGGEGVAW+GQAPF  DKHVFANLGDGTYFHSGLLAIRA+
Sbjct: 481  GIGCHYMTVWMDRSTSTFSQMGGEGVAWVGQAPFTNDKHVFANLGDGTYFHSGLLAIRAA 540

Query: 541  IAAGVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAI 600
            IA+  NITYKILYNDAVAMTGGQP+DG L+V  + +Q+AAEGA+KIV+VTDEP+KY A +
Sbjct: 541  IASKANITYKILYNDAVAMTGGQPVDGTLTVPQITHQLAAEGAKKIVIVTDEPQKYDANV 600

Query: 601  KLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFIND 660
             L  G+++HHRD+LD +QRELR++ G TILIYDQTCATEKRRRRKRG YPDPAKR  IN+
Sbjct: 601  GLAPGIDIHHRDKLDDVQRELRDIEGTTILIYDQTCATEKRRRRKRGAYPDPAKRVVINE 660

Query: 661  AVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKK 720
            AVCEGCGDCSV+SNCLSVEPLETE GTKRQINQS+CNKD+SC+ GFCPSFVT EG Q++K
Sbjct: 661  AVCEGCGDCSVQSNCLSVEPLETEYGTKRQINQSTCNKDYSCLKGFCPSFVTVEGGQLRK 720

Query: 721  PERHGVSMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLD 780
            P+  G++ + +P +P P +P +  PYGVLVTGVGGTGVVTIG LLGMAAHLE+KGVTVLD
Sbjct: 721  PKASGLASEAVPPVPDPEIPAITQPYGVLVTGVGGTGVVTIGALLGMAAHLESKGVTVLD 780

Query: 781  MAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTR 840
            + GLAQKGGAV+SHVQIA  P  +HATRIAMGEA+LVIGCD+IV+A D+ +S+ Q GRTR
Sbjct: 781  VTGLAQKGGAVMSHVQIANQPADIHATRIAMGEANLVIGCDSIVTASDECVSRMQSGRTR 840

Query: 841  AIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVG-EACDFINASGLAVALIGDAIFTNP 899
             ++N+A TPTAEFIKNP W+FPG SA+ D+R A G ++   ++A+  AVAL+GDAI+TNP
Sbjct: 841  VVLNSAPTPTAEFIKNPNWRFPGASADADIRAAAGDDSVSAVDANRFAVALLGDAIYTNP 900

Query: 900  LVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSL------T 953
             VLGYAWQKGWLPL+ ++L+RAIELN   VEKN+AAF+WGR  AHD   V  L      T
Sbjct: 901  FVLGYAWQKGWLPLTHESLIRAIELNAVQVEKNRAAFEWGRRAAHDLAAVRKLANLQDGT 960

Query: 954  GKLRNTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESAL 1013
                  A G+++V L T     L+ LI  RA++L AYQ+ AYA  +R  V  VRAAE+ L
Sbjct: 961  DDGNTNAAGSKIVSLHTPKA--LDTLIDKRAQYLVAYQNDAYATRYRKLVEEVRAAETKL 1018

Query: 1014 VGNGKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWL 1073
                  +PLTEA A+NL KLMAYKDEYEVARLY+DP F++KL+  FEG    D++L F L
Sbjct: 1019 GAADGQMPLTEAVAKNLHKLMAYKDEYEVARLYSDPAFIEKLKANFEG----DWKLRFHL 1074

Query: 1074 APPLMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEY 1133
            APP  A +D  GHLVK+++GP  +    VLAK+K LRG   D+FGKT ERRTERALI EY
Sbjct: 1075 APPATATKDTHGHLVKKQYGPWMLNAMHVLAKMKFLRGTALDMFGKTEERRTERALIVEY 1134

Query: 1134 RALLEELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPE 1191
              L+ EL  GL+A   A AI LA+LPD IRG+GHVKD+NL  VR +W +LL ++R PE
Sbjct: 1135 EVLVRELIGGLTAEKRALAIELANLPDGIRGYGHVKDNNLKSVRAKWASLLAKWRAPE 1192


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: 3623
Number of extensions: 141
Number of successful extensions: 4
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: 1200
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1153
Effective search space:  1325950
Effective search space used:  1325950
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