Alignments for a candidate for fruI in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Klebsiella michiganensis M5al

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate BWI76_RS10675 BWI76_RS10675 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::WCS417:GFF780
         (952 letters)



>FitnessBrowser__Koxy:BWI76_RS10675
          Length = 833

 Score =  322 bits (826), Expect = 5e-92
 Identities = 222/674 (32%), Positives = 342/674 (50%), Gaps = 26/674 (3%)

Query: 293 HGLHARPAKILAQLAKSFDGD---LRVRIVDGPVGAVSVKSLSKLLSLGARRGQVLEFIA 349
           +G+HARPA ++  L  +F      L +R      G  + KS   ++     +G   E I 
Sbjct: 13  NGVHARPASLVETLCNTFSSSVEWLNIRTE----GRGNAKSALAIIGTNTLKGDRCELIV 68

Query: 350 EPSIAGDALPALLAAVEEGLGEDVEPLPTLSVQPEVLDIEP--ELSAPLAGSQVQAIAAA 407
                  A  AL A + +       PLPT     E +D++P  E  + L  +   A+   
Sbjct: 69  SGEDEEQAFAALSAFIRDEFPHCDAPLPTA----EQMDVQPVPESLSRLNPTLFHALPVC 124

Query: 408 PGIAIGP-AHIQVLQVFDYPLRGESCAIERER--LHSALADVRRDIQGLIERSQSKAIRE 464
            G A G   H++ L + D      + AIE+E+  L   L  + ++I+  +  +   A   
Sbjct: 125 AGSAGGRLTHLKSLDLRDLGALPAAGAIEQEQAALDKGLTLLVKNIEFRLLDNDGTA-SA 183

Query: 465 IFVTHQEMLDDPELTDEVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALLAERAADLRD 524
           I   H+ +  D  L   +   L  G S   A ++  E    Q  +  ++ L ER  D+RD
Sbjct: 184 ILEAHRSLATDASLRQHLLDGLLSGLSCAEAVVASGEHFCAQFSASGNSYLQERVLDVRD 243

Query: 525 IGRRVLAQLCGVETSQEP---SEPYILVMDEVGPSDVARLDPARVAGILTARGGATAHSA 581
           +  ++L  + G      P   +E  I + DE+ PS    LD   + G+L   GG T+H+ 
Sbjct: 244 VCFQLLQHIYGEARFPAPGKLTEEAICLADELTPSQFLELDKTLLKGLLLRSGGTTSHTV 303

Query: 582 IVARALGIPALVGAGPAVLLLAAGTPLLLDGQRGRLHVDADAATLQRATVERDTREQRLQ 641
           I+AR+  IP LVG     LL      + +DG  G + V+ + A  +    E   + Q  +
Sbjct: 304 ILARSFNIPTLVGVDMEALLPWVDRRVQIDGNAGLVVVNPNQAVARYYQQEAWVQAQIRR 363

Query: 642 AASAQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAHPQAPDEA 701
              A   +   T DG  +EV ANI  S    +A   GA+ +GL RTE+++M  P AP E 
Sbjct: 364 QQQAWLDKEGRTEDGIRLEVAANIAHSVEATAAFNNGAQSVGLFRTEMLYMDRPSAPSEN 423

Query: 702 TQEAEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAEEENPFLGVRGIRLTLQRPQIME 761
                + + L+   GR +++RT+D+GGDKP+ Y  I  E NPFLG R +R+  +   +  
Sbjct: 424 ELYNIFCQALEPANGRGIIIRTMDIGGDKPVAYLNIPAENNPFLGYRAVRIYAEYQALFR 483

Query: 762 AQLRALLRSADNRPLRIMFPMVGSVDE--W--RAARDMTERLRLE-IPVAD-LQLGIMIE 815
            QLRA+LR++ +  L+IM PM+ S++E  W      D  + LR E IP  + + LGIM+E
Sbjct: 484 TQLRAILRASAHGALKIMIPMISSMEEILWVKEQLADAKQSLRSEHIPFDEKIPLGIMLE 543

Query: 816 VPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRA 875
           VPS   +     +E+DFFS+G+NDLTQY LA+DR +  ++   + L+PA L+ +D  V+A
Sbjct: 544 VPSVMFIIDQCCEEIDFFSIGSNDLTQYLLAVDRDNAKVTRHYNSLNPAFLRALDYAVQA 603

Query: 876 AHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIPEVKARVREFSLSEAQGLAQK 935
            H  GKW+G+CGEL A    +P+LVGLG+DELS+SA SIP  KAR+ +      + L  +
Sbjct: 604 VHRQGKWIGLCGELGAKGSVLPLLVGLGLDELSMSAPSIPATKARLAQLDSRACRQLLNQ 663

Query: 936 ALAVGSPAEVRALV 949
           A+   +  EV  L+
Sbjct: 664 AMQCRTSLEVEHLL 677



 Score = 53.9 bits (128), Expect = 4e-11
 Identities = 37/101 (36%), Positives = 52/101 (51%), Gaps = 6/101 (5%)

Query: 43  LQAREAQGSTFLGQGIAIPHGTPETRDQVFSTGVRLLQFPEGVDWGDGQ---IVYLAIGI 99
           L AREA  ST LG   AIPH   E  +Q   +  RL Q    V WGD +   ++ L +  
Sbjct: 731 LWAREAVFSTGLGFSFAIPHSKSEHIEQSTISVARLAQ---PVAWGDDEAQFVIMLTLNK 787

Query: 100 AAKSDEHLRLLQLLTRALGETDLGQALRRAGSAEALLKLLQ 140
            +  D+H+R+   L R +   +  Q+L  A S+EA+  LLQ
Sbjct: 788 HSAGDQHMRIFSRLARRIMHAEFRQSLVTAQSSEAIAALLQ 828


Lambda     K      H
   0.318    0.135    0.385 

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: 1395
Number of extensions: 68
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 952
Length of database: 833
Length adjustment: 43
Effective length of query: 909
Effective length of database: 790
Effective search space:   718110
Effective search space used:   718110
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 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