Alignments for a candidate for treEIIA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Caulobacter crescentus NA1000

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate CCNA_00571 CCNA_00571 phosphoenolpyruvate-protein phosphotransferase/phosphocarrier protein HPr/PTS system, glucose-specific IIA subunit

Query= reanno::WCS417:GFF4500
         (838 letters)



>FitnessBrowser__Caulo:CCNA_00571
          Length = 878

 Score =  634 bits (1634), Expect = 0.0
 Identities = 369/837 (44%), Positives = 506/837 (60%), Gaps = 30/837 (3%)

Query: 7   LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66
           L L APL G + AL++ PD VF+ R++GDGL IDP   TL AP  G + ++  + HAV++
Sbjct: 32  LVLTAPLQGWVSALEEAPDAVFAERMLGDGLAIDPLGSTLHAPCDGSVVSVHRARHAVTL 91

Query: 67  TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126
              NG ++LMH+GL+TV L G+GF   V+EGQ V+AG  LI  D D +A  ARSL+T ++
Sbjct: 92  RATNGAEILMHVGLETVALNGEGFEVFVEEGQTVKAGDRLIGLDLDLLAQRARSLITPVV 151

Query: 127 VVSGEPFSLLA---DGLVETGQPLLQLSP-SGAVEAVDEEEGDALFSKPLTLPNANGLHA 182
           + +GE F ++    D  +  GQ L++LSP +GA  A      D + ++ + +P A+G+HA
Sbjct: 152 ITNGEAFQIVRRDQDRQIGVGQFLMELSPIAGASRAAASGAADQI-TRQIIVPLAHGIHA 210

Query: 183 RPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKA 242
           RPAA  AQ AK F + + L    + ANA+S V +M+L    GDT+Q+ A+G DA+AA+ A
Sbjct: 211 RPAARIAQMAKTFASDLTLATGPRRANARSPVGLMSLAIRHGDTIQLLASGPDAQAAVTA 270

Query: 243 LVALLAEGCGEAVVNVAEPVATQSSAT-----------------LLRGVCASPGSAFGQV 285
           L  L+  G GE     A+  +T+++ T                 +L+GV A+PG A G+ 
Sbjct: 271 LAELIEGGMGEGAPVAAKTSSTKTAPTKTEPSEPPPPAPLPRDGVLKGVPAAPGLAIGKA 330

Query: 286 VQVTDPELVITEQGTGGATERAALTRGLLAANEALQVLQDKAAGS---AQAEIFRAHQEL 342
           V+++  E+V+ E G G A E AAL   L    E ++    KAA +   A+  I  AHQ  
Sbjct: 331 VRLSTAEIVVREAGEGVAHEEAALAVAL----ETVRARIGKAAETGDKARKAILAAHQAF 386

Query: 343 LEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKL 402
           L+DP L   AHRL+ EGKSA FAW  A    V   Q LG+  +AER  DL D+ ++VL+ 
Sbjct: 387 LDDPELYAGAHRLIAEGKSAGFAWRRAVGGYVQALQALGDRRMAERVDDLIDLERQVLRA 446

Query: 403 ILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPA 462
           + G +++   L   +IL+A++L PSQ    D   + GF T  GG TSHVAILA A+G+PA
Sbjct: 447 LSGEEETGAALAPGSILLADELLPSQLMGADPAALAGFATARGGPTSHVAILAAAMGVPA 506

Query: 463 ICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPA 522
           +  V   +  + +G  ++LDAD G L + P+   +E  + A   +  R     A A  PA
Sbjct: 507 LVAVGGALSKVKDGATLILDADAGTLRVAPDAKALEAAQTALAQRQQRKAAAKAAAHEPA 566

Query: 523 TTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIA 582
            TRDG  +EV AN  S+ + + A+  G EG GLLR+EFL+LDR   P  +EQA  Y AIA
Sbjct: 567 VTRDGVRIEVFANTGSVADAQAAVANGAEGSGLLRTEFLFLDRETPPDEDEQARQYQAIA 626

Query: 583 RALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILAS 642
            AL   R L++RTLDVGGDK   Y+P+ AE NP LGLRG+R+ L RP LL+ Q RAIL  
Sbjct: 627 EALDG-RPLIIRTLDVGGDKAAPYLPIPAEENPALGLRGVRVSLWRPHLLKAQLRAILRV 685

Query: 643 AGFARLHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPH 702
               +  IM+PMV+ L EL   R +LEE    LG+T+  +LG+MIE P+AA+ AD+ A  
Sbjct: 686 EPRGQCKIMVPMVASLDELRAVRAVLEEAKRELGITDRVQLGVMIETPAAAVTADLLAAE 745

Query: 703 VDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGAL 762
            DF SIGTNDLTQY LAMDR +P LA   D+ HPAVLR+I  T + A  H +WVGVCG L
Sbjct: 746 ADFLSIGTNDLTQYVLAMDRGNPELAAGIDALHPAVLRMIDQTCQGAARHHRWVGVCGGL 805

Query: 763 ASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVR 819
           AS+  A P+L+GLGV ELS +  + P +KA VR L L  C+ +A Q L       VR
Sbjct: 806 ASDLDATPILLGLGVAELSTTASIAPDVKARVRALSLEACRALAAQALEQTSPQAVR 862


Lambda     K      H
   0.318    0.133    0.371 

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: 1591
Number of extensions: 72
Number of successful extensions: 5
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: 838
Length of database: 878
Length adjustment: 42
Effective length of query: 796
Effective length of database: 836
Effective search space:   665456
Effective search space used:   665456
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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