Alignments for a candidate for fruI in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Cereibacter sphaeroides ATCC 17029

Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate WP_011840354.1 RSPH17029_RS02205 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::azobra:AZOBR_RS32325
         (846 letters)



>NCBI__GCF_000015985.1:WP_011840354.1
          Length = 838

 Score = 1018 bits (2631), Expect = 0.0
 Identities = 536/827 (64%), Positives = 627/827 (75%), Gaps = 9/827 (1%)

Query: 18  ELLRLSASPAGKEEAIREAAQLLIAAGCIDSAYAASMLRREAVANTFLGHGVAIPHGMVE 77
           EL++L A  + KEEAI +AA  L+AAGC+   + ASMLRREAV+NT+LG G+AIPHG VE
Sbjct: 13  ELIQLDARASSKEEAIAQAAAALVAAGCVRPGFEASMLRREAVSNTYLGKGIAIPHGTVE 72

Query: 78  DRGMVRRSGIAVLQVPGGIAWNPGQTAHLVVAIAAQSDAHIAVLRRLTRLMQDEARLTAL 137
           DR ++++  IAVLQV  G+ WN G+ A LVVAIAA+SD HI +LRRLTRL+QDE RL AL
Sbjct: 73  DRDLIQKDAIAVLQVRDGVEWNAGERARLVVAIAARSDGHIEILRRLTRLLQDEDRLAAL 132

Query: 138 FTVTDPAALAAAL-GEDAPVAAPATPGGDLAERFDWVVDYPTGLHARPATAWVETARASA 196
               D  AL+ AL G  A  AA A P GD A+ FDWV+DYPTGLHARPAT W E AR   
Sbjct: 133 AATDDRQALSDALNGVAAGAAATAEPAGDFAQSFDWVLDYPTGLHARPATEWAEAARRFP 192

Query: 197 ARIQVRHGDLVADAKALVALLQLGLRAGDSVVVSAEGDDAVAALARMKATITRLTAREKA 256
            RI++RHG   ADA+ +++LL LGL++GD++ VSAEG  A  ALA +K T+T L+AREKA
Sbjct: 193 CRIRIRHGAETADARNMISLLSLGLKSGDAITVSAEGQGAAEALATLKVTMTGLSAREKA 252

Query: 257 DAAAAAQKARAPVR--GWTPPNPLPAVPGIAASPGLAIGPVHVLPRAAVSVPDEPVPLIE 314
           DAA A +K RA     GW PP+   A+ G+ A+PG+AIG +  +    + +PDEPV L  
Sbjct: 253 DAARAEEKRRATAAAGGWVPPSSPRAIEGVPAAPGVAIGRITRIATDGMEIPDEPVELAR 312

Query: 315 GGDRLHEALSLTRQNLKALADDTARRLGPSEAAIFAAQAEILNDTDLVTLACQLMVEGHG 374
             D LH AL  T + L +LADDTARRLG S+AAIF AQA +L D DL+TLA Q +V+GHG
Sbjct: 313 AADLLHAALGQTAEQLHSLADDTARRLGESDAAIFRAQAGLLADPDLITLASQWLVDGHG 372

Query: 375 VAWSWHQAVERTAAGLAALDNPVLAARAADLRDVGQRVLARIDPALRTGGAPDLPDTPCI 434
           +AWSWH+A E  AA L+AL NPVLAARAADLRDVGQRVLA IDP        DLP+   I
Sbjct: 373 LAWSWHRAYEDMAARLSALRNPVLAARAADLRDVGQRVLAHIDPRFARSRLADLPEDT-I 431

Query: 435 LIAEDLSPSDTAALDMARVIGLATAQGGPTSHTAILARTLGLPAMVAGGAALMELANGTP 494
           L+AED+SPSD A LD A+V GL TA GGPTSHTAILARTLGLPA+V  GA +  L +G  
Sbjct: 432 LVAEDISPSDAAGLDPAKVAGLVTALGGPTSHTAILARTLGLPAVVGTGAVVERLEDGAC 491

Query: 495 AILDGQSGRLHLSPAAADIADARAWIAREEARKAEEEARRGLPARTRDGHEVEIGANVNR 554
           AI+DG  GRL+L P+ AD+A AR WIA EEAR+A     R LPA TRDGH ++IGAN+N 
Sbjct: 492 AIVDGHGGRLYLDPSEADLASARDWIAAEEARRARAAETRALPATTRDGHRIDIGANINL 551

Query: 555 PDQVAVALSQGAESVGLMRTEFLFLERGDAPGEDEQYETYRGMLTALEGRPLIVRALDIG 614
            +Q A AL QGAE VGLMRTEFLFLER ++P EDEQ E Y  M  ALEGRPL++RALDIG
Sbjct: 552 AEQAAFALGQGAEGVGLMRTEFLFLERSESPTEDEQAEAYAAMARALEGRPLVIRALDIG 611

Query: 615 GDKQVPHLQLPHEENPFLGVRGARLLLRRPELLETQLRALYRAAKDGGAKDGGALSIMFP 674
           GDKQV HL LP EENPFLGVRGARLLLRRP+LL  QLRALYRAA  GGA+    +S+MFP
Sbjct: 612 GDKQVAHLDLPREENPFLGVRGARLLLRRPDLLVPQLRALYRAAA-GGAQ----ISVMFP 666

Query: 675 MITALGEVQALRAACERIRAELDAPAVPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLT 734
           M+T+LGE+  LRA CERIR ELDAP VPLGIMVEVP+AA+ A   A H DFFSIGTNDLT
Sbjct: 667 MVTSLGELLELRATCERIRQELDAPVVPLGIMVEVPSAALLAAEFAAHADFFSIGTNDLT 726

Query: 735 QYALAIDRQHPELAAEADSLHPAVLRLIRLTVEGAERHGRWVGVCGGIAGDPFGAALLTG 794
           QYALAIDRQ+PELA EADSLHPAVLRLI LTV+GA  HGRWVGVCGGIAGDPFGAALL G
Sbjct: 727 QYALAIDRQNPELAPEADSLHPAVLRLIDLTVKGAAVHGRWVGVCGGIAGDPFGAALLAG 786

Query: 795 LGVRELSMTPRDIPAVKDRLRGSDLSALKDAAQRALDCETADAVRAL 841
           LGV ELSMTPRDIPAVK+RLR SD + L+  A+RAL C  A+AVRAL
Sbjct: 787 LGVDELSMTPRDIPAVKERLRQSDRAGLRALAERALACSDAEAVRAL 833


Lambda     K      H
   0.319    0.134    0.387 

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: 1946
Number of extensions: 88
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: 846
Length of database: 838
Length adjustment: 42
Effective length of query: 804
Effective length of database: 796
Effective search space:   639984
Effective search space used:   639984
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 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Apr 10 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 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