Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2C3

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate AO356_07335 AO356_07335 PTS fructose transporter subunit IIA

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_07335
          Length = 954

 Score =  512 bits (1318), Expect = e-149
 Identities = 308/672 (45%), Positives = 404/672 (60%), Gaps = 28/672 (4%)

Query: 169 SKPLTLPNANGLHARPAAVFAQAAKGFNASIYLH---KQTQSANAKSLVAIMALQTVQGD 225
           S  + L NA+GLHARPA + AQ AK F+  I +     Q  + +AKSL  +++L   +G 
Sbjct: 284 SARIGLANAHGLHARPAKILAQLAKSFDGEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQ 343

Query: 226 TLQVSAAGEDAEAAIKALVALLAEGCGEAVVNVAEPVATQS--------------SATLL 271
            L+  A    A  A+ AL+A + EG GE V  +  P A +               S +L+
Sbjct: 344 VLEFIAEPSIANDALPALLAAIEEGLGEEVEPLPPPSAPRETVMAEVATVMLAPESGSLI 403

Query: 272 RGVCASPGSAFG----QVVQVTDPELVITEQGTGGATERAALTRGLLAANEALQVLQDKA 327
           + V A+PG A G    QV+Q  D  L    +G   A ER  L   L      +Q L ++A
Sbjct: 404 QAVAAAPGIAIGPAHIQVLQAIDYPL----RGESAAIERERLQNALNQVRSDIQGLIERA 459

Query: 328 AGSAQAEIFRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAE 387
              A  EIF  HQE+L+DP L +     L  G+SA  AW     A     + L +AL+AE
Sbjct: 460 KAKAIREIFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVIEAAAKEQEALQDALLAE 519

Query: 388 RAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGA 447
           RAADL DVG+RVL  + G++    +  +  IL+ +++ PS  A LD  +V G +T  GGA
Sbjct: 520 RAADLRDVGRRVLAQLCGVETPN-EPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGA 578

Query: 448 TSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQ 507
           T+H AI+ARALG+PA+ G  A VL LA G  +LLD  +G LH++P+ A +++ +  R  +
Sbjct: 579 TAHSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDPDAATLQRAKEERDTR 638

Query: 508 VLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNR 567
             R +    Q   PA TRDGH VEV AN+     V  A+  G EG+GLLR+E +++  ++
Sbjct: 639 EQRLKVAAEQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAHSQ 698

Query: 568 APSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLE 627
           AP    Q   Y  +   L   R LVVRTLDVGGDKPL Y P+  E NPFLG+RGIRL L+
Sbjct: 699 APDEATQEAEYRKVLDGLAG-RPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQ 757

Query: 628 RPQLLREQFRAILASAGFARLHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMI 687
           RPQ++  Q RA+L SA    L IM PMV  + E   AR + E   L + + +L +LGIMI
Sbjct: 758 RPQVMEAQLRALLRSADSRPLRIMFPMVGSVDEWRQARAMTERLRLEIPVADL-QLGIMI 816

Query: 688 EVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVK 747
           EVPSAAL+A V A  VDFFS+GTNDLTQYTLA+DR HP L+ QAD  HPAVL+LI  TV+
Sbjct: 817 EVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVR 876

Query: 748 AAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIAR 807
           AAHAHGKWVGVCG LA++ LAVPVL+GLGVDELSVS   I  +KA VREL LA  Q +A+
Sbjct: 877 AAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIAEVKARVRELSLAQVQTLAQ 936

Query: 808 QVLGLEEAAEVR 819
             L +  A +VR
Sbjct: 937 AALAVGSADDVR 948


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: 1706
Number of extensions: 90
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: 954
Length adjustment: 43
Effective length of query: 795
Effective length of database: 911
Effective search space:   724245
Effective search space used:   724245
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