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_00457 CCNA_00457 phosphoenolpyruvate-protein phosphotransferase/phosphocarrier protein HPr/PTS system, glucose-specific IIA subunit

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



>FitnessBrowser__Caulo:CCNA_00457
          Length = 852

 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: 6   LVLTAPLQGWVSALEEAPDAVFAERMLGDGLAIDPLGSTLHAPCDGSVVSVHRARHAVTL 65

Query: 67  TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126
              NG ++LMH+GL+TV L G+GF   V+EGQ V+AG  LI  D D +A  ARSL+T ++
Sbjct: 66  RATNGAEILMHVGLETVALNGEGFEVFVEEGQTVKAGDRLIGLDLDLLAQRARSLITPVV 125

Query: 127 VVSGEPFSLLA---DGLVETGQPLLQLSP-SGAVEAVDEEEGDALFSKPLTLPNANGLHA 182
           + +GE F ++    D  +  GQ L++LSP +GA  A      D + ++ + +P A+G+HA
Sbjct: 126 ITNGEAFQIVRRDQDRQIGVGQFLMELSPIAGASRAAASGAADQI-TRQIIVPLAHGIHA 184

Query: 183 RPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKA 242
           RPAA  AQ AK F + + L    + ANA+S V +M+L    GDT+Q+ A+G DA+AA+ A
Sbjct: 185 RPAARIAQMAKTFASDLTLATGPRRANARSPVGLMSLAIRHGDTIQLLASGPDAQAAVTA 244

Query: 243 LVALLAEGCGEAVVNVAEPVATQSSAT-----------------LLRGVCASPGSAFGQV 285
           L  L+  G GE     A+  +T+++ T                 +L+GV A+PG A G+ 
Sbjct: 245 LAELIEGGMGEGAPVAAKTSSTKTAPTKTEPSEPPPPAPLPRDGVLKGVPAAPGLAIGKA 304

Query: 286 VQVTDPELVITEQGTGGATERAALTRGLLAANEALQVLQDKAAGS---AQAEIFRAHQEL 342
           V+++  E+V+ E G G A E AAL   L    E ++    KAA +   A+  I  AHQ  
Sbjct: 305 VRLSTAEIVVREAGEGVAHEEAALAVAL----ETVRARIGKAAETGDKARKAILAAHQAF 360

Query: 343 LEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKL 402
           L+DP L   AHRL+ EGKSA FAW  A    V   Q LG+  +AER  DL D+ ++VL+ 
Sbjct: 361 LDDPELYAGAHRLIAEGKSAGFAWRRAVGGYVQALQALGDRRMAERVDDLIDLERQVLRA 420

Query: 403 ILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPA 462
           + G +++   L   +IL+A++L PSQ    D   + GF T  GG TSHVAILA A+G+PA
Sbjct: 421 LSGEEETGAALAPGSILLADELLPSQLMGADPAALAGFATARGGPTSHVAILAAAMGVPA 480

Query: 463 ICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPA 522
           +  V   +  + +G  ++LDAD G L + P+   +E  + A   +  R     A A  PA
Sbjct: 481 LVAVGGALSKVKDGATLILDADAGTLRVAPDAKALEAAQTALAQRQQRKAAAKAAAHEPA 540

Query: 523 TTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIA 582
            TRDG  +EV AN  S+ + + A+  G EG GLLR+EFL+LDR   P  +EQA  Y AIA
Sbjct: 541 VTRDGVRIEVFANTGSVADAQAAVANGAEGSGLLRTEFLFLDRETPPDEDEQARQYQAIA 600

Query: 583 RALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILAS 642
            AL   R L++RTLDVGGDK   Y+P+ AE NP LGLRG+R+ L RP LL+ Q RAIL  
Sbjct: 601 EALDG-RPLIIRTLDVGGDKAAPYLPIPAEENPALGLRGVRVSLWRPHLLKAQLRAILRV 659

Query: 643 AGFARLHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPH 702
               +  IM+PMV+ L EL   R +LEE    LG+T+  +LG+MIE P+AA+ AD+ A  
Sbjct: 660 EPRGQCKIMVPMVASLDELRAVRAVLEEAKRELGITDRVQLGVMIETPAAAVTADLLAAE 719

Query: 703 VDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGAL 762
            DF SIGTNDLTQY LAMDR +P LA   D+ HPAVLR+I  T + A  H +WVGVCG L
Sbjct: 720 ADFLSIGTNDLTQYVLAMDRGNPELAAGIDALHPAVLRMIDQTCQGAARHHRWVGVCGGL 779

Query: 763 ASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVR 819
           AS+  A P+L+GLGV ELS +  + P +KA VR L L  C+ +A Q L       VR
Sbjct: 780 ASDLDATPILLGLGVAELSTTASIAPDVKARVRALSLEACRALAAQALEQTSPQAVR 836


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: 1557
Number of extensions: 70
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: 852
Length adjustment: 42
Effective length of query: 796
Effective length of database: 810
Effective search space:   644760
Effective search space used:   644760
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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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:

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:

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:

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:

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