GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ptsG in Pseudomonas simiae WCS417

Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate GFF4494 PS417_23000 PTS N-acetyl-D-glucosamine transporter

Query= BRENDA::P69786
         (477 letters)



>lcl|FitnessBrowser__WCS417:GFF4494 PS417_23000 PTS
           N-acetyl-D-glucosamine transporter
          Length = 568

 Score =  369 bits (946), Expect = e-106
 Identities = 201/476 (42%), Positives = 297/476 (62%), Gaps = 26/476 (5%)

Query: 1   MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMP 60
           M+++    LQ++G++LMLP+++LPIAG+LL +G  +   +      VM +AG ++FAN+ 
Sbjct: 1   MYQHFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIA-----VMHDAGQAIFANLA 55

Query: 61  LIFAIGVALGFT-NNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVL 119
           LIFAIG+A+GF  +N+G + LA  + Y +MV T+ V+   +              + G+L
Sbjct: 56  LIFAIGIAVGFARDNNGTAGLAGAIGYLVMVSTLKVMDTSI--------------NMGML 101

Query: 120 GGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAI 179
            GI SG +A  ++NRF  IKLPEYL FF G+RFVPI++G +A+  GV+   IWPPI   I
Sbjct: 102 AGIASGLMAGGLYNRFKDIKLPEYLAFFGGRRFVPIVTGFSAVGLGVIFGLIWPPIQHGI 161

Query: 180 QTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTN-AAGQVFHGDIP 238
            +F         + AF ++G   R L+  GLHHI N       G +T+   G V  GD+ 
Sbjct: 162 NSFGVLLMESGSLGAF-VFGVFNRLLIVTGLHHILNNMAWFVFGSFTDPVTGAVVTGDLT 220

Query: 239 RYMAGDPTAGK-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGIT 297
           RY AGDP  G+ ++G F   ++GLPAA +A++ +A PE R  +GGI +S ALTSFLTG+T
Sbjct: 221 RYFAGDPKGGQFMTGMFPVMLFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVT 280

Query: 298 EPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLF 357
           EPIEF+FMF+AP LY+IHA+L GL+  +  +L +  G +FS G ID ++  G S+  WL 
Sbjct: 281 EPIEFAFMFLAPFLYLIHAVLTGLSMAVTNMLNIHLGFTFSGGFIDMVLGWGKSTNGWLV 340

Query: 358 PIVGIGYAIVYYTIFRVLIKALDLKTPGREDA-TEDAKATGTSEMAPALVAAFGGKENIT 416
             VG+ YA++YY++F   I+  +LKTPGRED     A+A   ++ A A + A GG +N+ 
Sbjct: 341 FPVGLAYALIYYSVFNYCIRHFNLKTPGREDTQVVQAEAMSDNQRATAYIQALGGAQNLL 400

Query: 417 NLDACITRLRVSVADVSKVDQAGLKKLGAAGVVVAGSG--VQAIFGTKSDNLKTEM 470
           ++ AC TRLR+ + D +K   A LK LGA  VV  G+G  +Q + G  +D++  E+
Sbjct: 401 SVGACTTRLRLDMVDRNKAVDAELKALGAMAVVRPGNGGSLQVVVGPMADSIADEI 456



 Score = 39.7 bits (91), Expect = 3e-07
 Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 408 AFGGKENITNLDA-CITRLRVSVADVSKVDQAGLKKLGAAGVVVAGSGV-QAIFGTKSDN 465
           A GG+ N+  L+A  +TRLRV + D S + +A L  LG  GV    SGV   + G K+  
Sbjct: 491 ALGGRGNVRQLEAVAMTRLRVELGDDSGLSEADLTALGCQGVSQLESGVWHLLIGDKATG 550

Query: 466 LKTEMDEYI 474
           L   ++  +
Sbjct: 551 LGEALERLV 559


Lambda     K      H
   0.325    0.140    0.422 

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: 801
Number of extensions: 45
Number of successful extensions: 9
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: 477
Length of database: 568
Length adjustment: 35
Effective length of query: 442
Effective length of database: 533
Effective search space:   235586
Effective search space used:   235586
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: 40 (21.6 bits)
S2: 52 (24.6 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:

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:

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:

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, or view the source code.

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