Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate BWI76_RS11130 BWI76_RS11130 PTS glucose transporter subunit IIBC
Query= BRENDA::P69786 (477 letters) >FitnessBrowser__Koxy:BWI76_RS11130 Length = 477 Score = 918 bits (2372), Expect = 0.0 Identities = 462/477 (96%), Positives = 473/477 (99%) Query: 1 MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMP 60 MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMP Sbjct: 1 MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMP 60 Query: 61 LIFAIGVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLG 120 LIFAIGVALGFTNNDGVSALA+VVAYGIMVKTM+VVAPLVLHLPAEEIA+KHLADTGVLG Sbjct: 61 LIFAIGVALGFTNNDGVSALASVVAYGIMVKTMSVVAPLVLHLPAEEIAAKHLADTGVLG 120 Query: 121 GIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQ 180 GIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGV+LSFIWPPIG+AIQ Sbjct: 121 GIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVILSFIWPPIGTAIQ 180 Query: 181 TFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRY 240 TFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRY Sbjct: 181 TFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRY 240 Query: 241 MAGDPTAGKLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPI 300 MAGDPTAGKLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPI Sbjct: 241 MAGDPTAGKLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPI 300 Query: 301 EFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIV 360 EFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIV Sbjct: 301 EFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIV 360 Query: 361 GIGYAIVYYTIFRVLIKALDLKTPGREDATEDAKATGTSEMAPALVAAFGGKENITNLDA 420 GI YAIVYY +FRVLIKALDLKTPGREDATED+KA TSEMAPAL+AAFGGKENITNLDA Sbjct: 361 GICYAIVYYVVFRVLIKALDLKTPGREDATEDSKAGATSEMAPALIAAFGGKENITNLDA 420 Query: 421 CITRLRVSVADVSKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYIRNH 477 CITRLRVSVADV+KVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYIR++ Sbjct: 421 CITRLRVSVADVAKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYIRSN 477 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: 988 Number of extensions: 44 Number of successful extensions: 1 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: 477 Length adjustment: 33 Effective length of query: 444 Effective length of database: 444 Effective search space: 197136 Effective search space used: 197136 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: 51 (24.3 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