Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N1B4

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate Pf1N1B4_1146 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1146
          Length = 953

 Score =  504 bits (1299), Expect = e-147
 Identities = 302/672 (44%), Positives = 404/672 (60%), Gaps = 29/672 (4%)

Query: 169 SKPLTLPNANGLHARPAAVFAQAAKGFNASIYLH---KQTQSANAKSLVAIMALQTVQGD 225
           S  + L N +GLHARPA + AQ AK F   I +        + + KSL  +++L   +G 
Sbjct: 284 SARIALANTHGLHARPAKILAQLAKSFEGEIRVRIVDGHDSAVSVKSLSKLLSLGARRGQ 343

Query: 226 TLQVSAAGEDAEAAIKALVALLAEGCGEAV-------------VNVAEPVATQSSATLLR 272
            L+  A    A  A+ AL+A + EG GE V              +VAE +   +S +L++
Sbjct: 344 VLEFIAEPTIAADALPALLAAIEEGLGEEVEPLPAVSQHREVIADVAEVLLAPASGSLIQ 403

Query: 273 GVCASPGSAFG----QVVQVTDPELVITEQGTGGATERAALTRGLLAANEALQVLQDKAA 328
            + A+PG A G    QV QV D  L    +G   A ER  L + L      ++ L +++ 
Sbjct: 404 AIAAAPGIAIGPAHIQVQQVIDYPL----RGESAAIERERLKQALADVRRDIEGLIERSK 459

Query: 329 GSAQAEIFRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAER 388
             A  EIF  HQE+L+DP L +     L +G+SA  AW +   A     + L +AL+AER
Sbjct: 460 AKAIREIFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIEAAAKQQESLQDALLAER 519

Query: 389 AADLADVGQRVLKLILGIQDSAWDLPERA-ILIAEQLTPSQTASLDTRKVLGFVTVAGGA 447
           AADL D+G+RVL  + G++  A   PE+  IL+ +++ PS  A LD  +V G +T  GGA
Sbjct: 520 AADLRDIGRRVLAQLSGVETPAE--PEQPYILVMDEVGPSDVARLDPTRVAGILTARGGA 577

Query: 448 TSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQ 507
           T+H AI+ARALG+PA+ G  A VL L  G  +L+D  +G LH++ + A +++    R  +
Sbjct: 578 TAHSAIVARALGIPALVGAGAAVLLLKPGTPLLIDGQRGRLHVDADAATLQRATEERDTR 637

Query: 508 VLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNR 567
            LR +    Q   PA T DGH VEV AN+     V  A+  G EG+GLLR+E +++  ++
Sbjct: 638 ELRLKAAAEQRHQPALTTDGHAVEVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHSQ 697

Query: 568 APSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLE 627
           AP    Q   Y  +   L   R LVVRTLDVGGDKPL Y P+  E NPFLG+RGIRL L+
Sbjct: 698 APDEATQEVEYRRVLDGLAG-RPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQ 756

Query: 628 RPQLLREQFRAILASAGFARLHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMI 687
           RPQ++  Q RA+L +A    L IM PMV  + E   AR + E   L + + +L +LGIMI
Sbjct: 757 RPQVMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDMTERLRLEIPVADL-QLGIMI 815

Query: 688 EVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVK 747
           EVPSAAL+A V A  VDFFS+GTNDLTQYTLA+DR HP L+ QAD  HPAVL+LI  TV+
Sbjct: 816 EVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVR 875

Query: 748 AAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIAR 807
           AAHAHGKWVGVCG LA++ LAVPVL+GLGVDELSVS   I  +KA +REL L   Q +A+
Sbjct: 876 AAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSGRSIAEVKARIRELSLTQTQTLAQ 935

Query: 808 QVLGLEEAAEVR 819
           Q L +  A EVR
Sbjct: 936 QALAVGSANEVR 947


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: 1721
Number of extensions: 101
Number of successful extensions: 8
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: 953
Length adjustment: 43
Effective length of query: 795
Effective length of database: 910
Effective search space:   723450
Effective search space used:   723450
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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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