Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2E3

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate AO353_05485 AO353_05485 PTS fructose transporter subunit IIA

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



>FitnessBrowser__pseudo3_N2E3:AO353_05485
          Length = 953

 Score =  503 bits (1295), Expect = e-146
 Identities = 300/671 (44%), Positives = 402/671 (59%), Gaps = 27/671 (4%)

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

Query: 226 TLQVSAAGEDAEAAIKALVALLAEGCGE-------------AVVNVAEPVATQSSATLLR 272
            L++ A    A  A+ AL+  + EG GE              +  + + V   +S  +++
Sbjct: 344 VLELIAEPSIAADALPALLRAIEEGLGEDIEPLPTVSAQSEVIDEITDVVVAPASGCVIQ 403

Query: 273 GVCASPGSAFG----QVVQVTDPELVITEQGTGGATERAALTRGLLAANEALQVLQDKAA 328
            V A+PG A G    QV+Q  D  L    +G   A ER  L   L      ++ L  ++ 
Sbjct: 404 AVAAAPGIAIGPAHIQVLQAIDYPL----RGESTAIERERLKTSLADVRRDIEGLIQRSK 459

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

Query: 389 AADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGAT 448
           AADL D+G+RVL  + GI+  + +  +  IL+ +++ PS  A LD  +V G +T  GGAT
Sbjct: 520 AADLRDIGRRVLAQLCGIETPS-EPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGAT 578

Query: 449 SHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQV 508
           +H AI+ARALG+PA+ G  A VL LA+G  +LLD  +G LH++ + A +++    R ++ 
Sbjct: 579 AHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRAAEERDNRE 638

Query: 509 LRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRA 568
            R Q   AQ   PA T DGH VEV AN+     V  A+  G EG+GLLR+E +++   +A
Sbjct: 639 QRLQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAHQQA 698

Query: 569 PSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLER 628
           P    Q   Y  +   L   R LVVRTLDVGGDKPL Y P+  E NPFLG+RGIRL L+R
Sbjct: 699 PDEATQEVEYRRVLDGLAG-RPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQR 757

Query: 629 PQLLREQFRAILASAGFARLHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMIE 688
           PQ++  Q RA+L +A    L IM PMV  + E   AR + E   L + + +L +LGIMIE
Sbjct: 758 PQIMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDMTERLRLEIPVADL-QLGIMIE 816

Query: 689 VPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKA 748
           VPSAAL+A V A  VDFFS+GTNDLTQYTLA+DR HP L+ QAD  HPAVL+LI  TV+A
Sbjct: 817 VPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRA 876

Query: 749 AHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQ 808
           AHAHGKWVGVCG LA++ LAVPVL+GLGVDELSVS   I  +KA VREL LA  + +A+ 
Sbjct: 877 AHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIGEVKARVRELSLAQVKHLAQL 936

Query: 809 VLGLEEAAEVR 819
            L +  A EVR
Sbjct: 937 ALAVGSANEVR 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: 1693
Number of extensions: 90
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: 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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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