Alignments for a candidate for gamP in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for gamP in Pseudomonas simiae WCS417

Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate GFF4494 PS417_23000 PTS N-acetyl-D-glucosamine transporter

Query= BRENDA::P09323
         (648 letters)



>FitnessBrowser__WCS417:GFF4494
          Length = 568

 Score =  483 bits (1243), Expect = e-140
 Identities = 256/487 (52%), Positives = 335/487 (68%), Gaps = 18/487 (3%)

Query: 8   QRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGVASSWSKD 67
           QRLGRAL LPIA+LP+A LLLR G  DLLN+A +  AG AIF NLALIFAIG+A  +++D
Sbjct: 10  QRLGRALMLPIAILPIAGLLLRLGDTDLLNIAVMHDAGQAIFANLALIFAIGIAVGFARD 69

Query: 68  SAGAAALAGAVGYFVLTKAMVTINPEINMGVLAGIITGLVGGAAYNRWSDIKLPDFLSFF 127
           + G A LAGA+GY V+   +  ++  INMG+LAGI +GL+ G  YNR+ DIKLP++L+FF
Sbjct: 70  NNGTAGLAGAIGYLVMVSTLKVMDTSINMGMLAGIASGLMAGGLYNRFKDIKLPEYLAFF 129

Query: 128 GGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAGALGSGIFGFINRLLIPT 187
           GG+RFVPI TGF  + L  IFG +WPP+QH I++ G  ++ +G+LG+ +FG  NRLLI T
Sbjct: 130 GGRRFVPIVTGFSAVGLGVIFGLIWPPIQHGINSFGVLLMESGSLGAFVFGVFNRLLIVT 189

Query: 188 GLHQVLNTIAWFQIGEFTN-AAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLPGAAL 246
           GLH +LN +AWF  G FT+   G V  GD+ R++AGD   G FM+G FP+M+FGLP A L
Sbjct: 190 GLHHILNNMAWFVFGSFTDPVTGAVVTGDLTRYFAGDPKGGQFMTGMFPVMLFGLPAACL 249

Query: 247 AMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGISLFVA 306
           AMY  A  ERR ++GG+ LS+A+T+FLTGVTEP+EF FMFLAP LYL+HA+LTG+S+ V 
Sbjct: 250 AMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPFLYLIHAVLTGLSMAVT 309

Query: 307 TLLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKT 366
            +L IH GF+FS G ID  L +     S N W++  +G+ +  IY+ VF+  IR FNLKT
Sbjct: 310 NMLNIHLGFTFSGGFIDMVLGW---GKSTNGWLVFPVGLAYALIYYSVFNYCIRHFNLKT 366

Query: 367 PGREDKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVADSARV 426
           PGRED   ++V  EA S+      Q AT YI A+GG  NL ++ AC TRLRL + D  + 
Sbjct: 367 PGRED--TQVVQAEAMSD-----NQRATAYIQALGGAQNLLSVGACTTRLRLDMVDRNKA 419

Query: 427 NDTMCKRLGASGVVKL-NKQTIQVIVGAKAESIGDAMKKVVARGPVAAASAEATPATAAP 485
            D   K LGA  VV+  N  ++QV+VG  A+SI D + ++   G VAAA     P   AP
Sbjct: 420 VDAELKALGAMAVVRPGNGGSLQVVVGPMADSIADEI-RLAMPGFVAAA-----PVVVAP 473

Query: 486 VAKPQAV 492
           V KP AV
Sbjct: 474 VEKPVAV 480



 Score = 48.9 bits (115), Expect = 6e-10
 Identities = 24/86 (27%), Positives = 51/86 (59%), Gaps = 1/86 (1%)

Query: 391 QLATNYIAAVGGTDNLKAIDA-CITRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQV 449
           Q A  ++ A+GG  N++ ++A  +TRLR+ + D + +++     LG  GV +L      +
Sbjct: 483 QEAEKWLNALGGRGNVRQLEAVAMTRLRVELGDDSGLSEADLTALGCQGVSQLESGVWHL 542

Query: 450 IVGAKAESIGDAMKKVVARGPVAAAS 475
           ++G KA  +G+A++++V    + A++
Sbjct: 543 LIGDKATGLGEALERLVGAQQIGASA 568


Lambda     K      H
   0.324    0.139    0.408 

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: 987
Number of extensions: 59
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 648
Length of database: 568
Length adjustment: 37
Effective length of query: 611
Effective length of database: 531
Effective search space:   324441
Effective search space used:   324441
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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