Alignments for a candidate for ofo in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_02122 H281DRAFT_02122 indolepyruvate ferredoxin oxidoreductase

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



>FitnessBrowser__Burk376:H281DRAFT_02122
          Length = 1195

 Score = 1083 bits (2802), Expect = 0.0
 Identities = 574/1158 (49%), Positives = 766/1158 (66%), Gaps = 25/1158 (2%)

Query: 2    SLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLD 61
            +L++ +L D      G ++LTGTQAL RL ++Q   D+ARG+NT GFISGYRGSPLG +D
Sbjct: 12   ALSDYKLSDNLTATRGRIFLTGTQALVRLALMQRSLDRARGMNTAGFISGYRGSPLGMVD 71

Query: 62   KSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDR 121
            + LW+A+  L    I F P +NEEL  TAV G+Q+    P    +GVFAMWYGKGPGVDR
Sbjct: 72   QQLWKAKKLLSASDIRFLPAINEELGGTAVLGTQRVEADPERTVEGVFAMWYGKGPGVDR 131

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

Query: 182  YGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD- 240
            +G+ GW LSR+SG WV  K I+E V+S + V++D LR     PEDFE P  G+H RWPD 
Sbjct: 192  FGLYGWALSRFSGAWVGYKAISETVESGSTVDLDALRTDWSAPEDFEAPSGGLHNRWPDL 251

Query: 241  PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300
            P L  E R++  K+ A R FA+ N++++ +  SP+  +GI+T GK++LD+ + L  L L 
Sbjct: 252  PSLTIESRMHA-KLDAVRHFAKTNSIDKWIAPSPHANVGIVTCGKAHLDLMETLRRLDLT 310

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

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

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

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

Query: 541  RVDQLSRQIFHEGVKRIALVSDEPDKYPS-RDTFAPITSFHHRRELDAVQRELREFKGVS 599
             V Q++RQ+  EGV R  +VSDEP+KY    D F   T+FHHR E+D VQRELR+  GV+
Sbjct: 550  SVPQIARQVEAEGVSRFVVVSDEPEKYDGHHDLFPKGTTFHHRSEMDTVQRELRDTDGVT 609

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

Query: 660  REIDQNACNKDFSCVEGFCPSFVTVHGGGLRK-------PEAVAGGIEAATLPEPQHPTL 712
            R IDQ++CNKD+SCV GFCPSFVTV GG L+K       P+A+A  I A  LP  Q   L
Sbjct: 670  RRIDQSSCNKDYSCVNGFCPSFVTVEGGKLKKAAGAAFDPQALAERINALRLPATQ---L 726

Query: 713  D-RPWNVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQ 771
            D  P+++L+ GVGG+GV T+GAL+ MAAHLEGK  +VLD  G AQK G V + VR AA+ 
Sbjct: 727  DAAPYDILVTGVGGTGVVTVGALISMAAHLEGKSASVLDFMGFAQKGGSVLSFVRFAARD 786

Query: 772  SDIYAVRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQV 831
              +  VRI   +AD+LL CD++V A  ++L  +    +  VVN+H    A F +NPDA +
Sbjct: 787  EWLNQVRIDTQQADVLLACDMVVGASADALQTVRHGRTRIVVNTHAIPNATFVQNPDATL 846

Query: 832  PGAAMRQAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEK 891
               A+   +  A GA++    DA  LATR LGD+I  N+ +LG+A+Q GL+P+S  A+ +
Sbjct: 847  HADALIDKMRHAAGAERMSTCDAQALATRFLGDTIGANILMLGYAWQLGLVPVSFGALMR 906

Query: 892  AIELNGVSAKLNLQAFRWGRRAVLEREAVEQL--ARPVDMVEPICKTLEEIVDWRVDFLT 949
            AIELN V+ ++N  AF  GR A  +  A+E L  AR          TL+E++  R   L 
Sbjct: 907  AIELNNVAVQMNQLAFSIGRLAAEDPAALESLWQARHAAKQTVRIDTLDELIAHREGRLQ 966

Query: 950  RYQSAGLARRYRQLVERVRDADS---ADDLALSKAVARYYFKLLAYKDEYEVARLYSEPE 1006
             Y  A   +RYR LV+  R A+S   A+   +++AVA  +++LLA KDEYEVARL+++  
Sbjct: 967  IYGGASYVKRYRALVDAARRAESAIGANSERVTRAVATTFYRLLAVKDEYEVARLHTDAA 1026

Query: 1007 FRQQLEAQFEG----DYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFL 1062
            FR+ LEAQFEG    D+ + F+LAP  L  R      P K+  G W+  + GVLAK R L
Sbjct: 1027 FREALEAQFEGVAGKDFGINFNLAPPALT-RAHSGANPTKKTFGQWMWPVLGVLAKVRGL 1085

Query: 1063 RGTPLDPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVK 1122
            RGT LDPFG   +R++E +L  +YE T+   LA+L   N      +A L  ++RGYG VK
Sbjct: 1086 RGTMLDPFGRTLERKMEHELADDYETTLQRALAKLNADNLDDVAKLADLHARVRGYGHVK 1145

Query: 1123 ERSIAKARQQEKLLREQL 1140
              ++A  ++ E+ L  +L
Sbjct: 1146 LANLAGVKRGERDLAARL 1163


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: 2913
Number of extensions: 105
Number of successful extensions: 8
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: 1195
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1148
Effective search space:  1273132
Effective search space used:  1273132
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 17 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