Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate BPHYT_RS02745 BPHYT_RS02745 PTS system N-acetylglucosamine-specific transporter subunit IIBC
Query= BRENDA::P69786 (477 letters) >FitnessBrowser__BFirm:BPHYT_RS02745 Length = 591 Score = 376 bits (966), Expect = e-108 Identities = 207/484 (42%), Positives = 299/484 (61%), Gaps = 38/484 (7%) Query: 4 NAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVS-HVMAEAGGSVFANMPLI 62 N F +Q++G++LMLP++VLP+AG+LL +G P V + ++A+AGG++F N+PL+ Sbjct: 4 NPFLKIQRLGRALMLPIAVLPVAGLLLRLGQ------PDVFNIKMIADAGGAIFDNLPLL 57 Query: 63 FAIGVALGFT-NNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLGG 121 FAIGVA+GF +N+GV+ LA + Y I V M ++I K + GVL G Sbjct: 58 FAIGVAVGFAKDNNGVAGLAGAIGYLIEVAVM------------KDINDK--LNMGVLSG 103 Query: 122 IISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQT 181 I++G +A ++NR+ IKLP+YL FF GKRFVPI++G+ + G+ ++W P+ + I T Sbjct: 104 IVAGIVAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDT 163 Query: 182 FSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYM 241 W + AF ++G + R L+ GLHHI N G +T G GD+ R+ Sbjct: 164 AGHWLTTAGALGAF-VFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFF 222 Query: 242 AGDPTAGKLSGGFL-FKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPI 300 AGDPTAG GF M+GLPAA +A++H A E RA VGG++ S ALTSFLTG+TEPI Sbjct: 223 AGDPTAGTFMTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPI 282 Query: 301 EFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIV 360 EFSFMF+AP+LY+IHA+L G++ IC LG+ G +FS G ID+++ G S++ W + Sbjct: 283 EFSFMFLAPVLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPI 342 Query: 361 GIGYAIVYYTIFRVLIKALDLKTPGREDATED------------AKATGTS-EMAPALVA 407 G+ Y +VYY +FR I+ ++ TPGRE A D + GT+ A +A Sbjct: 343 GLVYMVVYYGLFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIA 402 Query: 408 AFGGKENITNLDACITRLRVSVADVSKVDQAGLKKLGAAGVVVAGS-GVQAIFGTKSDNL 466 A GG N++ +DAC TRLR+SV D +KV + LK +GA GV+ GS VQ I G ++D + Sbjct: 403 ALGGASNLSVVDACTTRLRLSVVDSNKVSENELKTIGARGVLKRGSTNVQVIIGPEADII 462 Query: 467 KTEM 470 E+ Sbjct: 463 ADEI 466 Score = 35.0 bits (79), Expect = 7e-06 Identities = 23/58 (39%), Positives = 30/58 (51%), Gaps = 7/58 (12%) Query: 406 VAAFGGKENITNLDA-CITRLRVSVADVSKVDQAGLKKLGAAGV------VVAGSGVQ 456 +A FGG N+ +LDA TRLR+ V D S VD+ L L A + +V G Q Sbjct: 513 LAVFGGAGNVLSLDAIAATRLRIVVRDPSAVDRQRLATLDTAWISADTFHIVVGDAAQ 570 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: 863 Number of extensions: 49 Number of successful extensions: 7 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: 591 Length adjustment: 35 Effective length of query: 442 Effective length of database: 556 Effective search space: 245752 Effective search space used: 245752 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