Alignments for a candidate for fruI in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Caulobacter crescentus NA1000

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate CCNA_00457 CCNA_00457 phosphoenolpyruvate-protein phosphotransferase/phosphocarrier protein HPr/PTS system, glucose-specific IIA subunit

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



>FitnessBrowser__Caulo:CCNA_00457
          Length = 852

 Score =  505 bits (1301), Expect = e-147
 Identities = 305/672 (45%), Positives = 399/672 (59%), Gaps = 11/672 (1%)

Query: 286 RITLANAHGLHARPAKILAQLAKSFDGDLRVRIVDGPVGAVSVKSLSKLLSLGARRGQVL 345
           +I +  AHG+HARPA  +AQ+AK+F  DL   +  GP  A + +S   L+SL  R G  +
Sbjct: 173 QIIVPLAHGIHARPAARIAQMAKTFASDLT--LATGPRRA-NARSPVGLMSLAIRHGDTI 229

Query: 346 EFIAEPSIAGDALPALLAAVEEGLGEDV----EPLPTLSVQPEVLDIEPELSAPLAGSQV 401
           + +A    A  A+ AL   +E G+GE      +   T +   +    EP   APL    V
Sbjct: 230 QLLASGPDAQAAVTALAELIEGGMGEGAPVAAKTSSTKTAPTKTEPSEPPPPAPLPRDGV 289

Query: 402 -QAIAAAPGIAIGPAHIQVLQVFDYPLRGESCAIERERLHSALADVRRDIQGLIERSQSK 460
            + + AAPG+AIG A             GE  A E   L  AL  VR  I G    +  K
Sbjct: 290 LKGVPAAPGLAIGKAVRLSTAEIVVREAGEGVAHEEAALAVALETVRARI-GKAAETGDK 348

Query: 461 AIREIFVTHQEMLDDPELTDEVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALLAERAA 520
           A + I   HQ  LDDPEL       + +G+SA  AW   +    +  ++L D  +AER  
Sbjct: 349 ARKAILAAHQAFLDDPELYAGAHRLIAEGKSAGFAWRRAVGGYVQALQALGDRRMAERVD 408

Query: 521 DLRDIGRRVLAQLCGVETSQEPSEP-YILVMDEVGPSDVARLDPARVAGILTARGGATAH 579
           DL D+ R+VL  L G E +     P  IL+ DE+ PS +   DPA +AG  TARGG T+H
Sbjct: 409 DLIDLERQVLRALSGEEETGAALAPGSILLADELLPSQLMGADPAALAGFATARGGPTSH 468

Query: 580 SAIVARALGIPALVGAGPAVLLLAAGTPLLLDGQRGRLHVDADAATLQRATVERDTREQR 639
            AI+A A+G+PALV  G A+  +  G  L+LD   G L V  DA  L+ A      R+QR
Sbjct: 469 VAILAAAMGVPALVAVGGALSKVKDGATLILDADAGTLRVAPDAKALEAAQTALAQRQQR 528

Query: 640 LQAASAQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAHPQAPD 699
             AA A  HEPA+TRDG  +EVFAN G  A   +AV  GAEG GLLRTE +F+     PD
Sbjct: 529 KAAAKAAAHEPAVTRDGVRIEVFANTGSVADAQAAVANGAEGSGLLRTEFLFLDRETPPD 588

Query: 700 EATQEAEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAEEENPFLGVRGIRLTLQRPQI 759
           E  Q  +Y+ + + L GRPL++RTLDVGGDK  PY PI  EENP LG+RG+R++L RP +
Sbjct: 589 EDEQARQYQAIAEALDGRPLIIRTLDVGGDKAAPYLPIPAEENPALGLRGVRVSLWRPHL 648

Query: 760 MEAQLRALLRSADNRPLRIMFPMVGSVDEWRAARDMTERLRLEIPVAD-LQLGIMIEVPS 818
           ++AQLRA+LR       +IM PMV S+DE RA R + E  + E+ + D +QLG+MIE P+
Sbjct: 649 LKAQLRAILRVEPRGQCKIMVPMVASLDELRAVRAVLEEAKRELGITDRVQLGVMIETPA 708

Query: 819 AALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHA 878
           AA+ A +LA E DF S+GTNDLTQY LA+DRG+P L+A  D LHPAVL++ID T + A  
Sbjct: 709 AAVTADLLAAEADFLSIGTNDLTQYVLAMDRGNPELAAGIDALHPAVLRMIDQTCQGAAR 768

Query: 879 HGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIPEVKARVREFSLSEAQGLAQKALA 938
           H +WVGVCG LA+D  A P+L+GLGV ELS +A   P+VKARVR  SL   + LA +AL 
Sbjct: 769 HHRWVGVCGGLASDLDATPILLGLGVAELSTTASIAPDVKARVRALSLEACRALAAQALE 828

Query: 939 VGSPAEVRALVE 950
             SP  VRALV+
Sbjct: 829 QTSPQAVRALVQ 840


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: 1737
Number of extensions: 93
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: 952
Length of database: 852
Length adjustment: 43
Effective length of query: 909
Effective length of database: 809
Effective search space:   735381
Effective search space used:   735381
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