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

GapMind for catabolism of small carbon sources

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

Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate AO353_04465 AO353_04465 PTS N-acetyl-D-glucosamine transporter

Query= TCDB::Q8GBT6
         (403 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04465
          Length = 571

 Score =  372 bits (956), Expect = e-107
 Identities = 187/392 (47%), Positives = 260/392 (66%), Gaps = 36/392 (9%)

Query: 4   LQRIGRSLMLPVAVLPAAALLVRLGNADMLGRPEFPAFVTKIAGFMAAGGNAILDNMALL 63
           LQR+GR+LMLP+A+LP A LL+RLG+ D+L               +   G  I  N+AL+
Sbjct: 9   LQRLGRALMLPIAILPIAGLLLRLGDTDLLN-----------IAIIHDAGQVIFANLALI 57

Query: 64  FAVGIAIGFAKKSDGSTALAAVVGYLVFKNVLATFTDKNLPQVAKAVDGKVVMVDAPVDA 123
           FA+GIA+GFA+ ++G+  LA  +GYLV  + L                    ++DA ++ 
Sbjct: 58  FAIGIAVGFARDNNGTAGLAGAIGYLVMVSTLK-------------------VLDASINM 98

Query: 124 KVLGGVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILSAFAGLVIGIVFGYIWPVLG 183
            +L G++ GL+   LY RF   KLP++  FFGGRR VPI + F+ + +G++FG IWP + 
Sbjct: 99  GMLAGIISGLMAGALYNRFKDIKLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQ 158

Query: 184 TGLHNFGEWLVGSGAVGAGIFGVANRALIPIGMHHLLNSFPWFQAGEYEGKS------GD 237
            G+++FG+ L+ SG++GA +FGV NR LI  G+HH+LN+  WF  G +   +      GD
Sbjct: 159 HGINSFGQLLLESGSIGAFVFGVFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGD 218

Query: 238 IARFLAGDPTAGQFMTGFFPIMMFALPAACLAIVHCARPERRKVVGGMMFSLALTSFVTG 297
           +AR+ AGDP  GQFMTG FP+M+F LPAACLA+   A PERRKV+GG+  S+ALTSF+TG
Sbjct: 219 LARYFAGDPKGGQFMTGMFPMMIFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTG 278

Query: 298 VTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWALGMKDGFGFSAGAVDFFLNLGIASNPW 357
           VTEPIEF FMF+AP+LY +H +LTG++MA+T AL +  GF FS GA+D  L  G ++N W
Sbjct: 279 VTEPIEFAFMFLAPLLYLLHVLLTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTNGW 338

Query: 358 GLALVGVCFAALYYVVFRFAITKFNLPTPGRE 389
            +  VG+ +A +YYVVF F I +FNL TPGRE
Sbjct: 339 LVFPVGLAYAVIYYVVFDFCIRRFNLKTPGRE 370


Lambda     K      H
   0.328    0.143    0.441 

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: 744
Number of extensions: 54
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: 403
Length of database: 571
Length adjustment: 34
Effective length of query: 369
Effective length of database: 537
Effective search space:   198153
Effective search space used:   198153
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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