Alignments for a candidate for ofo in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Burkholderia phytofirmans PsJN

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 BPHYT_RS02015 BPHYT_RS02015 MFS transporter

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



>FitnessBrowser__BFirm:BPHYT_RS02015
          Length = 1195

 Score = 1089 bits (2816), Expect = 0.0
 Identities = 577/1168 (49%), Positives = 773/1168 (66%), Gaps = 27/1168 (2%)

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

Query: 62   KSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDR 121
            + LW+A+  L    I F P +NEEL  TAV G+Q+    P    +GVFAMWYGKGPGVDR
Sbjct: 72   QQLWKAKKLLAASDIRFLPAINEELGGTAVLGTQRVESDPERTVEGVFAMWYGKGPGVDR 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+ GWELSR+SG WV  K I+E V+S + V++D LR    +P+DFE+P  G+H RWPD 
Sbjct: 192  FGLYGWELSRFSGAWVGYKAISETVESGSTVDLDALRTDWTMPQDFEVPAGGLHNRWPDL 251

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

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

Query: 361  RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAA 420
            RP VVG+  E G  LL +L EL P+ I  V A  LA    +   + R+  L A +  L+ 
Sbjct: 371  RPIVVGKNAEDGTLLLSSLGELRPSRILPVFANWLAKHKPALDRRERVVDLVAPQ-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 VQR+LR+  GV+
Sbjct: 550  SVPQIARQVEAEGVSRFVVVSDEPEKYDGHHDQFPKGTTFHHRSEMDTVQRQLRDTDGVT 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  +EA  LP P     
Sbjct: 670  RRIDQSSCNKDYSCVNGFCPSFVTVEGGKLKKAAGAAFDPQALAARVEA--LPIPATHLD 727

Query: 713  DRPWNVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQS 772
              P+++L+ GVGG+GV T+GAL+ MAAHLEGK  +VLD  G AQK G V + VR AA+  
Sbjct: 728  AAPYDILVTGVGGTGVVTVGALISMAAHLEGKSASVLDFMGFAQKGGSVLSFVRFAARDE 787

Query: 773  DIYAVRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVP 832
             +  VRI   +AD+LL CD++V A  ++L  +    +  VVN+H    A F  NPDA + 
Sbjct: 788  WLNQVRIDTQQADVLLACDMVVGASADALQTVRHGRTRIVVNTHAIPNATFVTNPDATLH 847

Query: 833  GAAMRQAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKA 892
              A+   +  A GA++    DA  LATR LGD+I  N+ +LG+A+Q GL+P+S  A+ +A
Sbjct: 848  ADALLDKMRHAAGAERMSTCDAQALATRFLGDTIGANILMLGYAWQLGLVPVSFGAMMRA 907

Query: 893  IELNGVSAKLNLQAFRWGRRAVLEREAVEQL--ARPVDMVEPICKTLEEIVDWRVDFLTR 950
            IELN V+ ++N  AF  GR A  +  A+E L  AR +        TL+E++  R   L  
Sbjct: 908  IELNNVAVQMNQLAFSIGRLAAEDPAALEALWQARHLAKQSVRVDTLDELIAHREGRLQT 967

Query: 951  YQSAGLARRYRQLVERVRDADSADDL---ALSKAVARYYFKLLAYKDEYEVARLYSEPEF 1007
            Y  A   +RYR LV+  R A+++ D     +++AVA  +++LLA KDEYEVARL+++  F
Sbjct: 968  YGGASYVKRYRALVDAARRAETSVDAKSERVTRAVATTFYRLLAVKDEYEVARLHTDAVF 1027

Query: 1008 RQQLEAQFEG----DYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLR 1063
            R+ LEAQFEG    D+ ++F+LAP  L + +P    P K+  G W+  + G LAKF  LR
Sbjct: 1028 REALEAQFEGVAGKDFGIKFNLAPPTLTRPEP-GKNPVKKTFGQWMWPVLGTLAKFSSLR 1086

Query: 1064 GTPLDPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKE 1123
            GT LDPFG   +R++ER+L  +YE T+   LA+L   N      +A L  ++RGYG VK 
Sbjct: 1087 GTMLDPFGRTLERKMERELAGDYETTLQRALARLDAGNLEDVAKLADLHARVRGYGHVKL 1146

Query: 1124 RSIAKARQQEKLLREQL----AKGDEVQ 1147
             ++A  ++ E+ L  +L    A G+ V+
Sbjct: 1147 ANLAGVKRGERDLAARLQIEAATGESVR 1174


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: 2957
Number of extensions: 108
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