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 trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate Pf1N1B4_833 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

Query= reanno::pseudo3_N2E3:AO353_15995
         (844 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_833
          Length = 844

 Score = 1272 bits (3292), Expect = 0.0
 Identities = 676/846 (79%), Positives = 731/846 (86%), Gaps = 4/846 (0%)

Query: 1   MTLTQPLQLLAPLSGVLMPLDHVPDPVFASRVIGDGLCIDPTSQVLCAPLAGVVSNLQHS 60
           M   Q LQLLAPLSGVLMPLD VPD VF+SRVIGDGLCIDPTSQ LCAPL GV+SN+Q S
Sbjct: 1   MATPQQLQLLAPLSGVLMPLDQVPDQVFSSRVIGDGLCIDPTSQTLCAPLTGVISNVQVS 60

Query: 61  GHAISITDDSGVQVLLHIGLDTVNLKGQGFSALVEQGQRVEAGQPLIEFDADYVALHARS 120
           GHA+SITDD+GVQVL+HIGLDTVNL G+GF+ LVE+GQRV  GQ LIEFDADY+ALHARS
Sbjct: 61  GHAVSITDDNGVQVLMHIGLDTVNLAGKGFTRLVEEGQRVIVGQALIEFDADYIALHARS 120

Query: 121 LLTLMLVVSGEPFSLLTPDSGLVACAQPVLRL--SLGDPRTVVAQEEGEALFSKPVHLPN 178
           LLTLMLVVSGEPF+ L P++G+V   QP+L L  S G     +AQE GEALFSKPV LPN
Sbjct: 121 LLTLMLVVSGEPFTWLAPETGVVESGQPLLSLNPSEGAADEGIAQE-GEALFSKPVTLPN 179

Query: 179 PNGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDA 238
            NGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQT HGD LQVSA G DA
Sbjct: 180 TNGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTAHGDVLQVSAAGADA 239

Query: 239 ELAISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQVAERT 298
           E+AI TLA+LLA GCGEAVT +A V  V  AQ  S  +LRGVCAS G+AFG VVQ+AE+T
Sbjct: 240 EVAIKTLAELLAAGCGEAVTLMAEVETVA-AQVSSLTVLRGVCASPGAAFGQVVQIAEQT 298

Query: 299 LEMPEFAADQQLERESLERALMHATQALQRLRDNAAGEAQADIFKAHQELLEDPSLLEQA 358
           LE+ E     Q+ERE L RAL  A  ALQ+LRD A G+AQADIFKAHQELLEDP LL+QA
Sbjct: 299 LEVSESGVSPQVEREHLSRALAKAVLALQQLRDKATGDAQADIFKAHQELLEDPGLLDQA 358

Query: 359 QALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILGVPDGVWE 418
            ALI  GKSA FAW +ATE+TATLFK LG+ LLAERA DL DVGQRVLKLILGV D   E
Sbjct: 359 LALIDAGKSAGFAWRAATESTATLFKKLGNALLAERAADLADVGQRVLKLILGVEDRAME 418

Query: 419 LPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVCGLPLQVLS 478
           LPD AILIAEQLTPSQTA LDT KVLGFATVGGGATSHVAILARA GLPA+CGLP+QVL+
Sbjct: 419 LPDGAILIAEQLTPSQTAGLDTRKVLGFATVGGGATSHVAILARASGLPAICGLPVQVLT 478

Query: 479 LASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAAVTRDGHHFEV 538
           L +GTRVLLDADKGEL LDP ++ IEQL A RQ Q+QR Q+EL NA  AA TRDGHH E+
Sbjct: 479 LINGTRVLLDADKGELQLDPELAAIEQLQANRQLQKQRQQYELANAGLAARTRDGHHVEI 538

Query: 539 TANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLV 598
           TAN+ASLAE EQAM+LG +G+GLLRSEFLY  R+ APSHDEQA TY AIARALGP RNLV
Sbjct: 539 TANIASLAEAEQAMALGGDGVGLLRSEFLYLDRNHAPSHDEQASTYGAIARALGPARNLV 598

Query: 599 VRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIML 658
           VRTLDVGGDKPLAYVPMD E NPFLGMRGIRLCLERPQLLR+QF+AILSSAGLARLHIML
Sbjct: 599 VRTLDVGGDKPLAYVPMDRETNPFLGMRGIRLCLERPQLLRDQFKAILSSAGLARLHIML 658

Query: 659 PMVSQLSELRLARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTND 718
           PMV+QLSELRLAR +LEEEALALGL ELPKLGIMIEVPAAALMADLFAPEVDFFSIGTND
Sbjct: 659 PMVTQLSELRLARQLLEEEALALGLTELPKLGIMIEVPAAALMADLFAPEVDFFSIGTND 718

Query: 719 LTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLL 778
           LTQYTLAMDRDHPRLASQADSFHPSVLRLIA+TVKAAHAHGKWVGVCGALASE LAVPLL
Sbjct: 719 LTQYTLAMDRDHPRLASQADSFHPSVLRLIATTVKAAHAHGKWVGVCGALASEKLAVPLL 778

Query: 779 LGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVREALSVQQQAMVET 838
           LGLGVDELSVSVPLIPAIKAA+REV+L DCQAIA QVLGLESAEQVREAL    +A V+T
Sbjct: 779 LGLGVDELSVSVPLIPAIKAAVREVDLLDCQAIAQQVLGLESAEQVREALRRHHEATVDT 838

Query: 839 SQVLES 844
           S VLE+
Sbjct: 839 SLVLEN 844


Lambda     K      H
   0.318    0.132    0.370 

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: 1858
Number of extensions: 81
Number of successful extensions: 4
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: 844
Length of database: 844
Length adjustment: 42
Effective length of query: 802
Effective length of database: 802
Effective search space:   643204
Effective search space used:   643204
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

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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