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.
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:
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