Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate AZOBR_RS32335 AZOBR_RS32335 PTS fructose transporter subunit IIBC
Query= BRENDA::O31645 (650 letters) >FitnessBrowser__azobra:AZOBR_RS32335 Length = 580 Score = 401 bits (1030), Expect = e-116 Identities = 213/477 (44%), Positives = 318/477 (66%), Gaps = 28/477 (5%) Query: 2 KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61 K++AITSCP GIAHT+MAAE +Q+AA LG +++VETQG +G + LTE+EIREAD ++I Sbjct: 113 KIVAITSCPTGIAHTFMAAEGIQQAAQALGHAVRVETQGSVGARDTLTEQEIREADVVLI 172 Query: 62 AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKAL-----NGDIPVYR---SATKSESG 113 AAD V+ RF GK++ G + I L+++AL +G P +A K+ Sbjct: 173 AADTQVDLARFAGKRVFKSGTKPAINDGRALVERALAEAQPHGTAPALADGVAAGKAAKA 232 Query: 114 NHQEKKQNPIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSFWKTIE- 172 H +++ Y+HLM GVSFM+PF+V GGLLIA+A LGG + + +DS T+ Sbjct: 233 EHAAAQRSGPYKHLMTGVSFMLPFVVTGGLLIAIAFALGG------IYVFEDSQQGTLGN 286 Query: 173 ---QIGS-ASFSFMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGI 228 QIG+ +F+ M+P LAGYIA+SIAD+PG+ PGM+GG +AA GAGFLGGI Sbjct: 287 ALFQIGAKGAFALMVPALAGYIAFSIADRPGITPGMVGGILAAN-------LGAGFLGGI 339 Query: 229 IAGFLAGYAALWIKK-LKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLT 287 +AGF+AGYA ++ + +++ K ++ + P++I+P+ SL+ GLA ++++GAPVA+ A+L+ Sbjct: 340 VAGFIAGYATSFLNRNIRLHKNLEGLKPVLILPLLGSLVTGLAMIYVVGAPVAEALATLS 399 Query: 288 VWLAGMKGSSSILLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIP 347 WL GM+GSS+ILL L++GAM++FDMGGPVNK A+ F + +I Y M A +P Sbjct: 400 AWLKGMQGSSAILLGLLIGAMMAFDMGGPVNKAAYAFSTGLIASQVYTPMAAAMAAGMVP 459 Query: 348 PIGLGIATFLGKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTG 407 P+GL +AT L +F +RE G AA +G+ ITEGAIPFAA+DPLRVIP+++ G+ Sbjct: 460 PLGLALATKLFADRFTREEREAGNAAGILGIAFITEGAIPFAARDPLRVIPALVLGAALT 519 Query: 408 SVIAMIGNVGDRVAHGGP-IVAVLGAVDHVLMFFIAVIAGSLVTALFVNVLKKDITA 463 I+M +V HGG ++ + AV H+ + +A++AG++ TA+ + LK+ +++ Sbjct: 520 GAISMGIGAELKVPHGGIFVLPIPNAVTHLAGYVVALVAGTVTTAVALRFLKRPVSS 576 Score = 48.9 bits (115), Expect = 6e-10 Identities = 27/95 (28%), Positives = 50/95 (52%) Query: 3 LLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIIIA 62 +LA+ + + +AAE L+KAA LG +I+VE + +GV N L + A +I+ Sbjct: 4 MLAVIAAGDLSTQAVLAAEALRKAAAALGHTIQVEVRSSLGVRNTLPTGAAQGAQGVILV 63 Query: 63 ADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKAL 97 + ++RF G K + + +R ++++AL Sbjct: 64 GSGDLGEERFAGLKRSAAALDAVLRDARAVLEQAL 98 Lambda K H 0.319 0.137 0.386 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: 807 Number of extensions: 49 Number of successful extensions: 6 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: 650 Length of database: 580 Length adjustment: 37 Effective length of query: 613 Effective length of database: 543 Effective search space: 332859 Effective search space used: 332859 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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