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 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_012399565.1 BPHY_RS00710 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000020045.1:WP_012399565.1
          Length = 1196

 Score = 1080 bits (2792), Expect = 0.0
 Identities = 572/1156 (49%), Positives = 758/1156 (65%), Gaps = 20/1156 (1%)

Query: 2    SLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLD 61
            +LA+ RL D      G ++LTGTQAL RL ++Q Q D+ARGLNT GFISGYRGSPLG +D
Sbjct: 12   ALADYRLSDNLTATRGRIFLTGTQALVRLTLMQRQLDKARGLNTAGFISGYRGSPLGMVD 71

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

Query: 122  AGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILD 181
            AGD  KH NA G S  GGVL++AGDDHGC SS++PHQS+ A IA  +PV+NP+NV ++L+
Sbjct: 132  AGDALKHGNAYGSSQHGGVLVVAGDDHGCVSSSMPHQSDFAMIAWHMPVVNPSNVADMLE 191

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

Query: 241  PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300
            P L  E+RL+  K+ A R FARAN++++ +  SP+  +GIIT GK++LD+ +AL  L L 
Sbjct: 252  PSLTIEQRLHA-KLDAVRHFARANSIDKWIAPSPHANVGIITCGKAHLDLMEALRRLDLT 310

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

Query: 361  RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAA 420
            RP + G+  E G+ LL +L EL P+ I  V A  LA    +   + R+  L A +  L+ 
Sbjct: 371  RPAIFGKHAEDGSMLLSSLGELRPSRILPVFANWLAKHKPALDRRERVVDLVAPQ-ILSN 429

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

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

Query: 541  RVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPI-TSFHHRRELDAVQRELREFKGVS 599
             V Q++RQ+  EGV    +VSDEP+KY       P  T+FHHR ELD VQRELR+  GV+
Sbjct: 550  SVPQIARQVEAEGVSHFVVVSDEPEKYDGHHGLFPKGTTFHHRSELDKVQRELRDIDGVT 609

Query: 600  VIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRK 659
            V+IYDQTCA EKRRRRK+G+  DP KR FIN  VCEGCGDCG +SNCL+V P+ET LGRK
Sbjct: 610  VLIYDQTCAAEKRRRRKKGEFPDPDKRLFINEEVCEGCGDCGVQSNCLSVEPVETPLGRK 669

Query: 660  REIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAA-----TLPEPQHPTLDR 714
            R IDQ++CNKD+SCV GFCPSFVT+ GG L+K   VA    A       LP P       
Sbjct: 670  RRIDQSSCNKDYSCVNGFCPSFVTIEGGKLKKAAGVAFDAAALATCVDALPLPTTQLDAA 729

Query: 715  PWNVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDI 774
            P+++L+ GVGG+GV T+GAL+ M AHLEGK  +VLD  G AQK G V + VR AA+   +
Sbjct: 730  PYDILVTGVGGTGVVTVGALISMGAHLEGKSASVLDFMGFAQKGGSVLSFVRFAARDEWL 789

Query: 775  YAVRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGA 834
              VRI   +AD+LL CD++V A  ++L  +    +  VVN+H    A F +NPDA +   
Sbjct: 790  NQVRIDTQQADVLLACDMVVGASADALQTVRRGRTRIVVNTHAIPNASFVQNPDANLHAD 849

Query: 835  AMRQAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIE 894
            A+   +  A G +     DA  LATR LGD+I  N+ +LGFA+Q GL+PIS  A+ +AIE
Sbjct: 850  ALLDKMRHAAGDEFMSSCDAQSLATRFLGDTIGANIVMLGFAWQLGLVPISFGAMMRAIE 909

Query: 895  LNGVSAKLNLQAFRWGRRAVLEREAVEQLARPVDMVEPI--CKTLEEIVDWRVDFLTRYQ 952
            LN V+ ++N  AF  GR A  +   +E L      V P    ++L+ ++  R   L  Y 
Sbjct: 910  LNNVAVQMNQLAFSIGRMAAADPAGLEVLWTQRHAVHPAVSLESLDALLADREARLHTYG 969

Query: 953  SAGLARRYRQLVERVRDA----DSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFR 1008
             A   +RYR LV+  R A    + A    LS+AVA  +++LLA KDEYEVARL+S+P FR
Sbjct: 970  GAAYVKRYRALVDAARQAERELEPASGERLSRAVATTFYRLLAVKDEYEVARLHSDPAFR 1029

Query: 1009 QQLEAQFEG----DYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRG 1064
              LEAQFEG    D+ ++F+LAP  ++ R     +P+K+  G W+  + G++AK+R LRG
Sbjct: 1030 AALEAQFEGVAGKDFGVKFNLAPPTIS-RAKHGAKPQKKTFGQWMWPVLGLMAKWRGLRG 1088

Query: 1065 TPLDPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKER 1124
            T LDPFG+  +RR+ER+L ++YE T+    A L        V +A L  ++RGYG VK  
Sbjct: 1089 TALDPFGHTVERRMERELSADYETTMQRAFAVLSHVTADDVVRLAELHARVRGYGHVKLA 1148

Query: 1125 SIAKARQQEKLLREQL 1140
            ++A  ++ E+ +  +L
Sbjct: 1149 NLAAVKRSEREIAARL 1164


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: 3028
Number of extensions: 106
Number of successful extensions: 6
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: 1196
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1149
Effective search space:  1274241
Effective search space used:  1274241
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 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