Alignments for a candidate for treEIIA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas simiae WCS417

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate GFF780 PS417_03965 PTS fructose transporter subunit IIA

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



>FitnessBrowser__WCS417:GFF780
          Length = 952

 Score =  509 bits (1310), Expect = e-148
 Identities = 313/706 (44%), Positives = 422/706 (59%), Gaps = 30/706 (4%)

Query: 134 SLLADGLVETGQPLLQLSPSGAV-EAVDEEEGDALFSKPLTLPNANGLHARPAAVFAQAA 192
           +LL +G    GQ L + + S AV E +  E      +  +TL NA+GLHARPA + AQ A
Sbjct: 251 ALLIEG---RGQELGRATSSRAVLEVLGGELPPDWPAARITLANAHGLHARPAKILAQLA 307

Query: 193 KGFNASIYLH---KQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKALVALLAE 249
           K F+  + +        + + KSL  +++L   +G  L+  A    A  A+ AL+A + E
Sbjct: 308 KSFDGDLRVRIVDGPVGAVSVKSLSKLLSLGARRGQVLEFIAEPSIAGDALPALLAAVEE 367

Query: 250 GCGE------------AVVNVAEPVATQSSATLLRGVCASPGSAFG----QVVQVTDPEL 293
           G GE             V+++   ++   + + ++ + A+PG A G    QV+QV D  L
Sbjct: 368 GLGEDVEPLPTLSVQPEVLDIEPELSAPLAGSQVQAIAAAPGIAIGPAHIQVLQVFDYPL 427

Query: 294 VITEQGTGGATERAALTRGLLAANEALQVLQDKAAGSAQAEIFRAHQELLEDPTLLEHAH 353
               +G   A ER  L   L      +Q L +++   A  EIF  HQE+L+DP L +   
Sbjct: 428 ----RGESCAIERERLHSALADVRRDIQGLIERSQSKAIREIFVTHQEMLDDPELTDEVD 483

Query: 354 RLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDL 413
             L +G+SA  AW S   A     + L +AL+AERAADL D+G+RVL  + G++ S  + 
Sbjct: 484 TRLKQGESAEAAWMSVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLCGVETSQ-EP 542

Query: 414 PERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLAL 473
            E  IL+ +++ PS  A LD  +V G +T  GGAT+H AI+ARALG+PA+ G    VL L
Sbjct: 543 SEPYILVMDEVGPSDVARLDPARVAGILTARGGATAHSAIVARALGIPALVGAGPAVLLL 602

Query: 474 ANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVT 533
           A G  +LLD  +G LH++ + A +++    R  +  R Q   AQ   PA TRDGH VEV 
Sbjct: 603 AAGTPLLLDGQRGRLHVDADAATLQRATVERDTREQRLQAASAQRHEPALTRDGHAVEVF 662

Query: 534 ANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVV 593
           AN+     V  A+  G EG+GLLR+E +++   +AP    Q   Y  +   L   R LVV
Sbjct: 663 ANIGESAGVASAVEQGAEGIGLLRTELIFMAHPQAPDEATQEAEYRRVLDGLAG-RPLVV 721

Query: 594 RTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLP 653
           RTLDVGGDKPL Y P+  E NPFLG+RGIRL L+RPQ++  Q RA+L SA    L IM P
Sbjct: 722 RTLDVGGDKPLPYWPIAEEENPFLGVRGIRLTLQRPQIMEAQLRALLRSADNRPLRIMFP 781

Query: 654 MVSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDL 713
           MV  + E   AR + E   L + + +L +LGIMIEVPSAAL+A V A  VDFFS+GTNDL
Sbjct: 782 MVGSVDEWRAARDMTERLRLEIPVADL-QLGIMIEVPSAALLAPVLAKEVDFFSVGTNDL 840

Query: 714 TQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLI 773
           TQYTLA+DR HP L+ QAD  HPAVL+LI  TV+AAHAHGKWVGVCG LA++ LAVPVL+
Sbjct: 841 TQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLV 900

Query: 774 GLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVR 819
           GLGVDELSVS   IP +KA VRE  L++ Q +A++ L +   AEVR
Sbjct: 901 GLGVDELSVSARSIPEVKARVREFSLSEAQGLAQKALAVGSPAEVR 946


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: 1745
Number of extensions: 92
Number of successful extensions: 7
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: 952
Length adjustment: 43
Effective length of query: 795
Effective length of database: 909
Effective search space:   722655
Effective search space used:   722655
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