Alignments for a candidate for treEIIA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas putida KT2440

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate PP_0793 PP_0793 Phosphotransferase system, fructose-specific EI/HPr/EIIA components

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



>FitnessBrowser__Putida:PP_0793
          Length = 950

 Score =  491 bits (1263), Expect = e-142
 Identities = 311/710 (43%), Positives = 414/710 (58%), Gaps = 28/710 (3%)

Query: 136 LADGLVE-TGQPLLQLSPSGAVEAVDEEEGDALF-SKPLTLPNANGLHARPAAVFAQAAK 193
           L + L+E  GQ L Q + S AV  V   E  A + S  + L N +GLHARPA V AQ AK
Sbjct: 249 LCEVLIEGRGQVLYQATSSRAVLEVLGGEVPADWPSARVVLANPHGLHARPAKVLAQLAK 308

Query: 194 GFNASIYLH---KQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKALVALLAEG 250
           GF   I +        + + KSL  +++L   +G  L++ A    A  A+  L+A + +G
Sbjct: 309 GFEGEIRVRLVDSAQPAVSVKSLSKLLSLGARRGQALELVAEPSIAADALPVLLAAIEQG 368

Query: 251 CGEAVVNVAEPVA-----------TQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQG 299
            GE V  + + VA             ++ + ++GV A+PG A G      + E     +G
Sbjct: 369 LGEEVEPLPQSVAPIADDVPEVLQAPAAGSRIQGVGAAPGIASGPAHVCVEREFDYPLRG 428

Query: 300 TGGATERAALTRGLLAANEALQVL---QDKAAGSAQAEIFRAHQELLEDPTLLEHAHRLL 356
              A ER  L   L   N  LQ L    DKA G    EIF  HQE+L DP L +   + L
Sbjct: 429 ESCALERQKLREALATVNGELQALVLRSDKAIG----EIFVTHQEMLADPALTDDVEQRL 484

Query: 357 GEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPER 416
            +G+SAA AW +   A     + L +AL+AERAADL D+G+RVL  + G+Q  A   PE+
Sbjct: 485 AQGESAAAAWMAVIEAAARQQEALHDALLAERAADLRDIGRRVLAQLCGVQ--AQVEPEQ 542

Query: 417 A-ILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALAN 475
             +L+  ++ PS  A LD  +V G VT  GGAT+H AI+ARALG+PA+ G  A +L L +
Sbjct: 543 PYVLVMTEVGPSDVARLDPNRVAGIVTAQGGATAHSAIVARALGIPAVVGAGASILLLES 602

Query: 476 GKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTAN 535
           G  +LLD  +G + + P   E+++  A R  +  R Q   A    PA TRDGH VEV AN
Sbjct: 603 GTPLLLDGQRGVVSVAPPADELQRALAERDLREQRLQAAWANRFEPAITRDGHAVEVFAN 662

Query: 536 VASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRT 595
           +     +   +  G EGVGLLR+E +++   +AP    Q   Y  +   L   R LVVRT
Sbjct: 663 IGDSNGIAKVVEQGAEGVGLLRTELIFMAHPQAPDVATQEAEYRRVLDGLDG-RPLVVRT 721

Query: 596 LDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMV 655
           LDVGGDKPL Y P+ AE NPFLG+RG+RL L+RPQ++ +Q RA+L +A    L IM PMV
Sbjct: 722 LDVGGDKPLPYWPIAAEENPFLGVRGVRLTLQRPQVMEDQLRALLRAADQRPLRIMFPMV 781

Query: 656 SLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQ 715
             + E   AR ++E     + + +L +LGIM+EVPSAAL+A   A  VDFFSIGTNDLTQ
Sbjct: 782 GQVHEWREARAMVERLRAEIPVADL-QLGIMVEVPSAALLAAQLAREVDFFSIGTNDLTQ 840

Query: 716 YTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGL 775
           YTLA+DR HP L+ QAD  HPAVL LI  TV+AAHAHGKWVGVCG LA++  AV VL+GL
Sbjct: 841 YTLAIDRGHPSLSAQADGLHPAVLSLIDMTVRAAHAHGKWVGVCGELAADPQAVAVLLGL 900

Query: 776 GVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQY 825
            VDELSVS   I  +KA VR+ D    + +AR+ L  + AA VR  + +Y
Sbjct: 901 DVDELSVSARSIAEVKALVRQADHQTARALAREALQQDSAAAVRALVERY 950


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: 1708
Number of extensions: 87
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: 950
Length adjustment: 43
Effective length of query: 795
Effective length of database: 907
Effective search space:   721065
Effective search space used:   721065
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