GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__WCS417:GFF4494
          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:

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