Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate H281DRAFT_02007 H281DRAFT_02007 phosphoenolpyruvate--protein phosphotransferase
Query= TCDB::Q9HY55 (956 letters) >FitnessBrowser__Burk376:H281DRAFT_02007 Length = 582 Score = 295 bits (754), Expect = 8e-84 Identities = 200/577 (34%), Positives = 295/577 (51%), Gaps = 23/577 (3%) Query: 403 LQAIAASPGIASGPAHVQVAQRFEFQPRGESPAH---ERERLLRAKRAVDEEIVGLVERS 459 L I S GIA G A++ + PA E ER A++ V EE+ L Sbjct: 5 LHGIPVSRGIAIGRAYLIAPAALDVDHYLIEPAQIESEVERFRAAQQRVHEELDALRADL 64 Query: 460 TVKAIREI--FVT-HREMLDDPELAEQ-VQLRLNRGESAEAAWSRVVEDSAAQQEALHDA 515 A E+ F+ H +L+D L ++ + L R + E A + +E + + + D Sbjct: 65 AADAPSEMGAFINVHSMILNDAMLVQETIDLIRTRRYNVEWALTEQLERLSRHFDDIEDE 124 Query: 516 LLAERAADLRDLGRRVLARLCG-----VEAPREPEQPYILVMDEVGPSDVARLDAQRVAG 570 L ER AD+ + RVL L G V I+V ++ P+D+ + Q G Sbjct: 125 YLRERKADIEQVVERVLKALAGASGSLVNGVHGACDEMIVVAHDIAPADMMQFKTQTFQG 184 Query: 571 ILTARGGATSHSAIIARALGIPALVGAGAAVLGLEPGTALLLDGEHGWLQVAPSTEQLQQ 630 +T GG TSH+AI+AR+LGIPA VG A + +++DG+HG + V P+ L++ Sbjct: 185 FVTDLGGRTSHTAIVARSLGIPAAVGVQHASALIRQDDLIIVDGDHGIVIVDPAPIVLEE 244 Query: 631 AAAERDARQQRQARADAQRLEPARTRDGHAVEVCANLGDTAGAARAVELGAEGVGLLRTE 690 + + + Q + + P +T G +E+CAN+ A AV+ GA GVGL RTE Sbjct: 245 YSYRQSEKALEQRKLQRLKFSPTQTLCGTRIELCANIELPEDARAAVDAGATGVGLFRTE 304 Query: 691 FVFMNNA-RAPDLATQEAEYRRVLDALDGRPLVARTLDVGGDKPLPYWP----IPHEENP 745 F+FMN+ R P+ Q YRR ++ ++G P+ RT+DVG DKPL NP Sbjct: 305 FLFMNHKHRMPEEEEQFEAYRRAVELMNGLPVTIRTIDVGADKPLDSMSGGDGYETAANP 364 Query: 746 YLGLRGIRLTLQRPQILETQLRALFRAAGERPLRVMFPMVGSLDEWRQARDLALRLREEI 805 LGLR IR +L PQ+ TQLRA+ RA+ ++++ PM+ E Q DL + ++ Sbjct: 365 ALGLRAIRWSLSEPQMFLTQLRAILRASAFGTVKILVPMLAHAQEIDQTLDLIREAKRQL 424 Query: 806 PLA------DLQLGIMVEVPSAALLAPVLAREVDFFSVGTNDLTQYTLAIDRGHPSLSAQ 859 A ++Q+G M+E+P+AA+ P+ + +DF S+GTNDL QYTLAIDR S++ Sbjct: 425 DDAGIAYDPNVQVGAMIEIPAAAIALPLFLKRLDFLSIGTNDLIQYTLAIDRADNSVAHL 484 Query: 860 ADGLHPAVLQLIDMTVRAAHAEGKWVGVCGELAADPLALPLLVGLGVDELSVSARSIALV 919 D LHPAVL LI T+R A G V VCGE+A DP LL+G+G+ E S+ + +V Sbjct: 485 YDPLHPAVLHLIAFTLREAKRAGVPVSVCGEMAGDPSLTRLLLGMGLTEFSMHPSQLLVV 544 Query: 920 KAGVRELQLVAARGLARKALGLASAAEVRALVEAEVQ 956 K V L L EV+A ++ Q Sbjct: 545 KQEVLRSHLKTLEKPVADVLASFEPEEVQAALKRVAQ 581 Lambda K H 0.318 0.134 0.382 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: 920 Number of extensions: 38 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: 956 Length of database: 582 Length adjustment: 40 Effective length of query: 916 Effective length of database: 542 Effective search space: 496472 Effective search space used: 496472 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 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