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 trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate AO353_15995 AO353_15995 PTS mannose transporter subunit IIC

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



>FitnessBrowser__pseudo3_N2E3:AO353_15995
          Length = 844

 Score = 1612 bits (4173), Expect = 0.0
 Identities = 844/844 (100%), Positives = 844/844 (100%)

Query: 1   MTLTQPLQLLAPLSGVLMPLDHVPDPVFASRVIGDGLCIDPTSQVLCAPLAGVVSNLQHS 60
           MTLTQPLQLLAPLSGVLMPLDHVPDPVFASRVIGDGLCIDPTSQVLCAPLAGVVSNLQHS
Sbjct: 1   MTLTQPLQLLAPLSGVLMPLDHVPDPVFASRVIGDGLCIDPTSQVLCAPLAGVVSNLQHS 60

Query: 61  GHAISITDDSGVQVLLHIGLDTVNLKGQGFSALVEQGQRVEAGQPLIEFDADYVALHARS 120
           GHAISITDDSGVQVLLHIGLDTVNLKGQGFSALVEQGQRVEAGQPLIEFDADYVALHARS
Sbjct: 61  GHAISITDDSGVQVLLHIGLDTVNLKGQGFSALVEQGQRVEAGQPLIEFDADYVALHARS 120

Query: 121 LLTLMLVVSGEPFSLLTPDSGLVACAQPVLRLSLGDPRTVVAQEEGEALFSKPVHLPNPN 180
           LLTLMLVVSGEPFSLLTPDSGLVACAQPVLRLSLGDPRTVVAQEEGEALFSKPVHLPNPN
Sbjct: 121 LLTLMLVVSGEPFSLLTPDSGLVACAQPVLRLSLGDPRTVVAQEEGEALFSKPVHLPNPN 180

Query: 181 GLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDAEL 240
           GLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDAEL
Sbjct: 181 GLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDAEL 240

Query: 241 AISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQVAERTLE 300
           AISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQVAERTLE
Sbjct: 241 AISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQVAERTLE 300

Query: 301 MPEFAADQQLERESLERALMHATQALQRLRDNAAGEAQADIFKAHQELLEDPSLLEQAQA 360
           MPEFAADQQLERESLERALMHATQALQRLRDNAAGEAQADIFKAHQELLEDPSLLEQAQA
Sbjct: 301 MPEFAADQQLERESLERALMHATQALQRLRDNAAGEAQADIFKAHQELLEDPSLLEQAQA 360

Query: 361 LIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILGVPDGVWELP 420
           LIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILGVPDGVWELP
Sbjct: 361 LIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILGVPDGVWELP 420

Query: 421 DQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVCGLPLQVLSLA 480
           DQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVCGLPLQVLSLA
Sbjct: 421 DQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVCGLPLQVLSLA 480

Query: 481 SGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAAVTRDGHHFEVTA 540
           SGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAAVTRDGHHFEVTA
Sbjct: 481 SGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAAVTRDGHHFEVTA 540

Query: 541 NVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLVVR 600
           NVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLVVR
Sbjct: 541 NVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLVVR 600

Query: 601 TLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPM 660
           TLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPM
Sbjct: 601 TLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPM 660

Query: 661 VSQLSELRLARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLT 720
           VSQLSELRLARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLT
Sbjct: 661 VSQLSELRLARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLT 720

Query: 721 QYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLG 780
           QYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLG
Sbjct: 721 QYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLG 780

Query: 781 LGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVREALSVQQQAMVETSQ 840
           LGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVREALSVQQQAMVETSQ
Sbjct: 781 LGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVREALSVQQQAMVETSQ 840

Query: 841 VLES 844
           VLES
Sbjct: 841 VLES 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: 2134
Number of extensions: 78
Number of successful extensions: 1
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.

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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