Alignments for a candidate for treEIIA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas fluorescens GW456-L13

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate PfGW456L13_4832 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4832
          Length = 838

 Score =  633 bits (1632), Expect = 0.0
 Identities = 369/832 (44%), Positives = 504/832 (60%), Gaps = 18/832 (2%)

Query: 7   LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66
           L L APLSG +L L KVPD VF+S  +GDG+ IDP + TL AP AGV+ ++  +GHAV++
Sbjct: 8   LTLSAPLSGPVLTLAKVPDAVFASGAMGDGIAIDPLNDTLHAPCAGVVVHVARTGHAVTL 67

Query: 67  TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126
             DNG ++L+H+GLDTV L GQGF+ LV+EG RV  GQPL+ +D D VA   +SL++L++
Sbjct: 68  RADNGAELLLHLGLDTVELQGQGFSMLVKEGARVSNGQPLLRYDLDKVAQQCKSLVSLLI 127

Query: 127 VVSGEPFSLLADGL--VETGQPLLQLSPSGAVEAVDEEE--GDALFSKPLTLPNANGLHA 182
           + + + F      L  V+ G+PLL +     V A  + E  G+ +    + + +  GLHA
Sbjct: 128 LTNSQDFQARPITLKSVKVGEPLLHIIRRQGVGAQADVELAGEEVVGH-IRIAHRGGLHA 186

Query: 183 RPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKA 242
           RPAA+  Q A+GF +   LH   +SA   SL+ +M L   +   +QVS  G DAEAA++A
Sbjct: 187 RPAALIRQTAQGFKSKSQLHFAGKSATCDSLIGLMGLAIGEQAEVQVSCQGPDAEAALQA 246

Query: 243 LVALLAEGCGEAVVNVAEPVATQ----SSATLLRGVCASPGSAFGQVVQVTDPELVITEQ 298
           L+  L+    E     A     Q    + A +L GVCA+PG   G +  +    L +   
Sbjct: 247 LLTALSTALAEDSHAAAPTTIAQRNRPAEAGVLHGVCAAPGLVGGPLFHLNAISLPVDAG 306

Query: 299 GTGGATERAALTRGLLAANEALQ---VLQDKAAGSAQAEIFRAHQELLEDPTLLEHAHRL 355
                 ++  L   L      ++   VL  K   +A+  IF AH  LLEDP LL+ A + 
Sbjct: 307 HHDPQQQQQVLDAALSQVRSEIERTLVLAKKHKDTAEEAIFAAHLALLEDPALLDAAIQT 366

Query: 356 LGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAW--DL 413
           + +G +A  AW+ A      + Q  G+ L+AERA DL D+ QRVL+ +LG     W  D+
Sbjct: 367 VAQGTAATHAWSQAIDVQCEVLQQTGSTLLAERANDLRDLKQRVLRALLG---DTWHYDV 423

Query: 414 PERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLAL 473
           P  AI+ A +LTPS    L  + V G     GGATSHVAILAR  GLP +  + + +L  
Sbjct: 424 PAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCMVALGSTLLDQ 483

Query: 474 ANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVT 533
             G+ V+LDAD G L L P+   +  +   ++ Q  R     AQA  PA T DG  +EV 
Sbjct: 484 QQGQPVVLDADGGRLELTPSAERLADVRQLQQQQQQRRAEQQAQAHTPALTTDGLRIEVA 543

Query: 534 ANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVV 593
           ANVAS  E   AL  G +GVGLLR+EFL++DR+ AP  +EQ   Y A+  A+G ++++++
Sbjct: 544 ANVASSTEAADALANGADGVGLLRTEFLFVDRHTAPDEQEQHHAYQAVLDAMG-DKSVII 602

Query: 594 RTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLP 653
           RT+DVGGDK L Y+P+ AE NP LGLRGIRL   RP+LL +Q RA+L     +R  I+LP
Sbjct: 603 RTIDVGGDKQLDYLPLPAEANPVLGLRGIRLAQARPELLDQQLRALLHLRPLSRCRILLP 662

Query: 654 MVSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDL 713
           MV+ + EL    + L+     LGL + P+LG+MIEVP+AAL+A+  A H DF SIGTNDL
Sbjct: 663 MVTEVDELLHIHQRLDALCGELGLAQRPELGVMIEVPAAALLAEQLAEHADFLSIGTNDL 722

Query: 714 TQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLI 773
           +QYTLAMDRDH  LA + D+ HPA+LRLIA T   A  H +WVGVCGALAS+ LA PVLI
Sbjct: 723 SQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAQHNRWVGVCGALASDPLATPVLI 782

Query: 774 GLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQY 825
           GLGV ELSVS   +  IK  VR LD ++C+ I++ +L L  A+ VR A  Q+
Sbjct: 783 GLGVSELSVSPVQVGEIKDRVRHLDASECRRISQGLLKLSSASAVRHACHQH 834


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: 73
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: 838
Length of database: 838
Length adjustment: 42
Effective length of query: 796
Effective length of database: 796
Effective search space:   633616
Effective search space used:   633616
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

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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