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_012404781.1 BPHY_RS27730 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000020045.1:WP_012404781.1
          Length = 1195

 Score = 1730 bits (4481), Expect = 0.0
 Identities = 843/1200 (70%), Positives = 995/1200 (82%), Gaps = 20/1200 (1%)

Query: 1    MNAP---LTPPVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGL 57
            MNAP   +T   SD +     NV+L+DKYTLE+GRVYISGTQALVRLPMLQ+ RD  AGL
Sbjct: 1    MNAPDRAVTSEQSDPL-----NVTLDDKYTLEKGRVYISGTQALVRLPMLQKARDLKAGL 55

Query: 58   NTAGFISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDA 117
            NTAGFISGYRGSPLGALDQSLWKAK+HL A+DIVFQ G+NEDLAAT+VWG+QQ+N++P A
Sbjct: 56   NTAGFISGYRGSPLGALDQSLWKAKKHLQANDIVFQPGVNEDLAATAVWGTQQINLWPGA 115

Query: 118  RFEGVFGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIF 177
              +GVFGMWYGKGPGVDRT DVF+HANSAGS   GGVLVLAGDDHAAKSS++AHQSEH F
Sbjct: 116  TRDGVFGMWYGKGPGVDRTGDVFRHANSAGSDARGGVLVLAGDDHAAKSSSVAHQSEHAF 175

Query: 178  KACGLPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVL 237
             A G+PVLYP+NVQEYLDYGLH WAMSRYSGLWV+MKCVTDV+ES+AS++LDP RV+IV 
Sbjct: 176  IAAGIPVLYPANVQEYLDYGLHGWAMSRYSGLWVAMKCVTDVIESTASIDLDPDRVDIVT 235

Query: 238  PQDFILPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTG 297
            P D+ +P GGLNIRWPD PL QEARLLD KWYA LAY+RAN+++R+ IDS   RFGI+T 
Sbjct: 236  PTDYAMPAGGLNIRWPDAPLAQEARLLDEKWYAALAYIRANRLNRVVIDSDKPRFGIITA 295

Query: 298  GKAYLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQ 357
            GKAYLD RQAL++LGLDD+TCARIG+R+ KVGCVWPL+A  ARAFA GL+EILVVEEKRQ
Sbjct: 296  GKAYLDVRQALSDLGLDDDTCARIGLRVLKVGCVWPLDAQDARAFATGLEEILVVEEKRQ 355

Query: 358  IMEYALKEELYNWRDDVRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIA 417
            I+EYALKEELYNWR+DVRPK+YGKFDE+DN GGEWS+P+ +WLLPAHYELSPA+IA+AIA
Sbjct: 356  ILEYALKEELYNWREDVRPKIYGKFDERDNEGGEWSVPRGDWLLPAHYELSPALIAKAIA 415

Query: 418  TRLDKFELPADVRARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSR 477
             RL + +LP DVRAR+ AR+A+IEAKE+  A PRVA ERKPWFCSGCPHNTST VPEGSR
Sbjct: 416  RRLARADLPKDVRARMLARVAIIEAKEREAAKPRVAVERKPWFCSGCPHNTSTRVPEGSR 475

Query: 478  ALAGIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAI 537
            ALAGIGCHYM++WMDR T TFSQMGGEGVAWIGQ  F+GD+HVF NLGDGTYFHSGLLAI
Sbjct: 476  ALAGIGCHYMSMWMDRKTETFSQMGGEGVAWIGQMHFSGDRHVFVNLGDGTYFHSGLLAI 535

Query: 538  RASIAAGVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYS 597
            RA+IAA  NITYK+LYNDAVAMTGGQP+DG L+V  +A+QV AEGA+++V+VTDEP+KY 
Sbjct: 536  RAAIAANANITYKVLYNDAVAMTGGQPVDGVLTVPQIAHQVHAEGAKRVVIVTDEPQKYR 595

Query: 598  AAIKLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAF 657
              I LP GV+VHHRD+LD +QR LR++PG T+LIYDQTCATEKRRRRKRGTYPDPA+RAF
Sbjct: 596  TGIVLPAGVDVHHRDQLDTVQRTLRDIPGTTVLIYDQTCATEKRRRRKRGTYPDPARRAF 655

Query: 658  INDAVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQ 717
            INDAVCEGCGDCS +SNCLSVEPL+T LGTKR+INQSSCNKDFSCVNGFCPSFVTAEGAQ
Sbjct: 656  INDAVCEGCGDCSEQSNCLSVEPLDTPLGTKRKINQSSCNKDFSCVNGFCPSFVTAEGAQ 715

Query: 718  VKKP------ERHGVSMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHL 771
            ++KP      +  G    +  ALP P+LP L  PYG+LVTGVGGTGVVTIGGL+GMAAH+
Sbjct: 716  LRKPKAAGGDKSAGAGKIDFDALPAPSLPALAKPYGILVTGVGGTGVVTIGGLIGMAAHI 775

Query: 772  ENKGVTVLDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVI 831
            E+KGVTVLDMAGLAQKGGAVLSHVQ+A+ P+ LHATRIA GEA LVIGCDAIVSA +DV+
Sbjct: 776  EHKGVTVLDMAGLAQKGGAVLSHVQLASAPEALHATRIATGEARLVIGCDAIVSASNDVL 835

Query: 832  SKTQVGRTRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVGEACDFINASGLAVALI 891
            S+TQ G T A +N+  TPTAEF+KNPKW FPG   E ++R+++G+ C FI+A+ LA+ L+
Sbjct: 836  SRTQHGVTCAAINSGATPTAEFVKNPKWTFPGTQTEAELRDSIGDGCAFIDANALALTLL 895

Query: 892  GDAIFTNPLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLS 951
            GD I++NPL+LG+AWQKGWLPL L +L+RAIELN  +VEKN+ AF+WGR++A   +  + 
Sbjct: 896  GDTIYSNPLLLGFAWQKGWLPLQLSSLLRAIELNAVSVEKNQQAFNWGRYIAQHGDDAVR 955

Query: 952  LTGKLRNTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAES 1011
              GK    A  A V+++P S    L+ LIA R   L +YQ+ AYA+ +R  +  +RA E 
Sbjct: 956  ALGK-PAAAPQAIVMRIPES----LDHLIASREALLKSYQNEAYARKYRRVIDGIRAKEM 1010

Query: 1012 ALVGNGKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNF 1071
               G+ K LPLT A A NL+KLMAYKDEYEVARLY DP +L+KLR QFEGEPGRDY+L+F
Sbjct: 1011 EFGGDSK-LPLTRAIATNLAKLMAYKDEYEVARLYADPAYLEKLRQQFEGEPGRDYKLSF 1069

Query: 1072 WLAPPLMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIG 1131
            +LAPPL AKRDE+GHL K+RFGP  +  F VLA++KGLRG  FDVFGKT ERR ER LI 
Sbjct: 1070 YLAPPLFAKRDERGHLQKKRFGPWMLPAFRVLARMKGLRGTAFDVFGKTVERRGERQLIA 1129

Query: 1132 EYRALLEELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPE 1191
            EY AL++E    L++   A A+ LA LPDDIRGFGHVK+ NL     +   LL  +R PE
Sbjct: 1130 EYIALVDEFCATLTSDRLAVALQLACLPDDIRGFGHVKERNLQAAAKKKERLLADYRTPE 1189


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: 3562
Number of extensions: 123
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: 1195
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1148
Effective search space:  1320200
Effective search space used:  1320200
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