Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate WP_078430180.1 BK574_RS22665 glucose-specific PTS transporter subunit IIBC
Query= BRENDA::P69786 (477 letters) >NCBI__GCF_002019605.1:WP_078430180.1 Length = 656 Score = 478 bits (1229), Expect = e-139 Identities = 250/481 (51%), Positives = 331/481 (68%), Gaps = 15/481 (3%) Query: 1 MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMP 60 MFK AF LQ+VG++LM PVSVLP AG+LLG+G N +P +MAEAGG +F N+ Sbjct: 1 MFKKAFGTLQRVGRALMTPVSVLPAAGLLLGLGHENVLDIP-----IMAEAGGVIFGNLA 55 Query: 61 LIFAIGVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLA--DTGV 118 L+FA+GVA+G + DGV+ LAAV+ Y +M T+ ++A + AE + + TGV Sbjct: 56 LLFAVGVAIGLADGDGVAGLAAVIGYLVMNTTLGIMAG---YYGAETVTVLGIETLQTGV 112 Query: 119 LGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSA 178 GGII G +AA ++ RFY I+LP +LGFFAGKRFVPII+ A+ G++ F+WPPI Sbjct: 113 FGGIIMGLVAAALYKRFYNIELPPFLGFFAGKRFVPIITAATAVLLGIIFVFVWPPIQGV 172 Query: 179 IQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIP 238 I FS A VA ++GF +R L+PFGLHHI+ PF + G +TNAAG V GD+ Sbjct: 173 IDWFSHLATETGTTVAAFVFGFTQRALIPFGLHHIFYQPFWFEFGTFTNAAGDVVRGDMT 232 Query: 239 RYMAGDPTAGK-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGIT 297 R+ AGDPTAG ++G F F ++GLPAAA+AI+H A+PE + V GIM SAALTSFLTGIT Sbjct: 233 RFFAGDPTAGTFMAGLFPFMLFGLPAAALAIYHEARPERKKAVAGIMASAALTSFLTGIT 292 Query: 298 EPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLF 357 EPIEF+F+FVAP+L++IH I AG +F I LLG++ G +FS G ID+++ G S+ WL Sbjct: 293 EPIEFAFLFVAPVLFLIHCIFAGFSFVIMDLLGVKAGFTFSGGFIDYVLYWGLSTNSWLI 352 Query: 358 PIVGIGYAIVYYTIFRVLIKALDLKTPGR----EDATEDAKATGTSEMAPALVAAFGGKE 413 VGI + VYY FR I+ +LKTPGR E +E+ G E+A ++ A GGK+ Sbjct: 353 IPVGIAFGFVYYFGFRFAIRKWNLKTPGREPKEEQVSEEVAKGGKRELASNVLHALGGKQ 412 Query: 414 NITNLDACITRLRVSVADVSKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEY 473 NIT LDACITRLRVSV + S+VD A LKKLGA+GV+ G+ +QAIFGT+SD LK ++ + Sbjct: 413 NITALDACITRLRVSVKEPSEVDSAQLKKLGASGVLEMGNNIQAIFGTQSDALKGQIKDL 472 Query: 474 I 474 I Sbjct: 473 I 473 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: 949 Number of extensions: 51 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: 656 Length adjustment: 36 Effective length of query: 441 Effective length of database: 620 Effective search space: 273420 Effective search space used: 273420 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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