Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate WP_038857764.1 AFK65_RS05470 PTS transporter subunit EIIC
Query= BRENDA::P69786 (477 letters) >NCBI__GCF_001277175.1:WP_038857764.1 Length = 499 Score = 353 bits (905), Expect = e-101 Identities = 202/487 (41%), Positives = 284/487 (58%), Gaps = 32/487 (6%) Query: 2 FKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPL 61 F + + L +G++LMLP+S+LP AG+LL G LP +M AGG +F N+PL Sbjct: 7 FVKSLSKLSMIGRALMLPISLLPAAGLLLAFGDKFH--LP-----LMMNAGGVIFDNLPL 59 Query: 62 IFAIGVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEE-----IASKHLADT 116 +FAIG A+G + G++AL+A V+ I+ T++ + + A + Sbjct: 60 LFAIGSAVGLASESGIAALSAAVSVFIINITISTQLGITPEMAASGGKYAMVVGIPTLQM 119 Query: 117 GVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIG 176 GV GG+ISG +AA+ +NRF+ ++LPE+LGFF+GKRFV I + + G+ L ++W I Sbjct: 120 GVFGGLISGILAAWCYNRFHTLQLPEFLGFFSGKRFVAIAAAFLSFLLGLALPYVWQHIQ 179 Query: 177 SAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGD 236 + I S N + I+G +ER L+P GLHHIW F G+YT GQV HGD Sbjct: 180 AGIDALSVIVNGDNQAASTFIFGLVERALIPLGLHHIWYPSFWYSFGDYTTQTGQVIHGD 239 Query: 237 -----------IPRYMAGD-PTAGK-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGI 283 + + + AGK + G F ++ LPAA +A++H A +N+ GI Sbjct: 240 QTIWFKMLEEGVKSFSSNTYQNAGKFMQGEFPLMLFALPAACLAMYHEASTKNKKIASGI 299 Query: 284 MISAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLID 343 + SAALT FLTGITEP+EF+F+FVAP+LY+ +AI+AGLA+ LL SFS GLID Sbjct: 300 LFSAALTCFLTGITEPVEFTFIFVAPVLYVFNAIMAGLAYMCMYLLDAHIAKSFSAGLID 359 Query: 344 FI------VLSGNSSKLWLFPIVGIGYAIVYYTIFRVLIKALDLKTPGREDATEDAKATG 397 +I +G + IVGI AI+YY FR +I+ D+KTPGR D T A Sbjct: 360 YISFGILPSFNGYQTHYLNAVIVGIPMAIIYYFTFRFVIRRFDVKTPGRVDVTASADDKT 419 Query: 398 TSEMAPALVAAFGGKENITNLDACITRLRVSVADVSKVDQAGLKKLGAAGVVVAG-SGVQ 456 +E+A +V GGKENIT++ ACITRLR+ VA VD+ GL LGA GVV G +G+Q Sbjct: 420 DAELAGNIVGLLGGKENITSVGACITRLRLEVARPDLVDKDGLNGLGARGVVFVGDNGIQ 479 Query: 457 AIFGTKS 463 IFG ++ Sbjct: 480 VIFGARA 486 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: 699 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 477 Length of database: 499 Length adjustment: 34 Effective length of query: 443 Effective length of database: 465 Effective search space: 205995 Effective search space used: 205995 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 24 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