Align protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized)
to candidate BWI76_RS07290 BWI76_RS07290 PTS beta-glucoside transporter subunit EIIBCA
Query= BRENDA::P27219 (456 letters) >FitnessBrowser__Koxy:BWI76_RS07290 Length = 626 Score = 249 bits (637), Expect = 1e-70 Identities = 150/455 (32%), Positives = 241/455 (52%), Gaps = 10/455 (2%) Query: 1 MDFEQISRSLLPLLGGKENIASAAHCATRLRLVLVDDALADQQAIGKIDGVKGCFRNAGQ 60 M++ + + +L +GG ENI HCATRLR+ D A + IG + GV GQ Sbjct: 1 MNYNETADKILHAVGGAENIRMLTHCATRLRMEFNDRAKVNDAQIGTLPGVISVVEKGGQ 60 Query: 61 MQIIFGTGVVNKVYAAFIQAAGISESSKSEAADLAAKKLNPFQRIARLLSNIFVPIIPAI 120 QI+ G V +VY +A + E D AK RI ++S F P+IPAI Sbjct: 61 FQIVIGNEV-QQVYRRLNKA--LPEKKGPAGGDKNAKPAGIVARIISVISTTFTPVIPAI 117 Query: 121 VASGLLMGLLGMVKTYGWVDPSNALYIMLDMCSSAAFIILPILIGFTAAREFGGNPYLGA 180 +G++ LL ++K G + +++ Y +L++ + AAF LP+L+ + A+ +F NP L Sbjct: 118 TGAGMIKALLAILKLTGVISETSSTYQLLNIIADAAFFFLPVLLAYGASLKFECNPILAM 177 Query: 181 TLGGILTHPALTNAWGVAAGFHTMNFFGIEVAMIGYQGTVFPVLLAVWFMSMVEKRLRRV 240 TL G+L HP + +AAG ++F GI V + Y G+V P++L VW MS VE+ +V Sbjct: 178 TLAGVLLHPGIGQM--LAAG-KAVDFVGINVLLSDYAGSVLPIILTVWLMSWVERFAEKV 234 Query: 241 IPDALDLILTPFLTVIISGFIALLLIGPAGRALGDGISFILSTLISHAGWLAGLLFGGLY 300 P + + P L ++I+ +AL+++GPAG L D ++ + HA WL +L G L Sbjct: 235 SPSIIKFFVKPMLILLITAPLALVVVGPAGILLNDLVAAGAGAIDRHASWLIPMLMGTLQ 294 Query: 301 SVIVITGIHHSFHAIEAGLLGNPSIGVNFLLPIWAMANVAQGGACFAVWFKTKDAKIKAI 360 ++ITG + I G L + P +NVA G A V KTK++ ++ + Sbjct: 295 PFLIITGTAWAMTPIATGQLSKSGYEM-INGPGMLASNVAMGAATLCVALKTKNSNLRQL 353 Query: 361 TLPSAFSAMLGITEAAIFGINLRFVKPFIAALVGGAAGGAWV-VS--MHVYMTAVGLTAI 417 S F+A+LGITE A++G+ L+F + IAA++GG G + VS + + GL A+ Sbjct: 354 ASSSGFTALLGITEPALYGVLLKFRRVLIAAMIGGGCAGVYAGVSGLVRYAFVSPGLAAL 413 Query: 418 PGMAIVQASSLLNYIIGMAIAFAVAFALSLTLKYK 452 P ++++ ++ AI+ V F L+ + +K Sbjct: 414 PAFIGENPMNIVHALVTCAISIVVTFTLTWFIAFK 448 Lambda K H 0.327 0.141 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: 663 Number of extensions: 40 Number of successful extensions: 4 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: 456 Length of database: 626 Length adjustment: 35 Effective length of query: 421 Effective length of database: 591 Effective search space: 248811 Effective search space used: 248811 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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