Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate BPHYT_RS02575 BPHYT_RS02575 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::psRCH2:GFF3291 (960 letters) >FitnessBrowser__BFirm:BPHYT_RS02575 Length = 582 Score = 290 bits (743), Expect = 1e-82 Identities = 197/575 (34%), Positives = 294/575 (51%), Gaps = 33/575 (5%) Query: 408 VNGIAASPGIAIGPVLVRKPQVIDY------PKRGESPVIELQRLDAALDKVHADIGTL- 460 ++GI S GIAIG + P +D P + ES E++R A VH ++ TL Sbjct: 5 LHGIPVSRGIAIGRAYLIAPAALDVDHYLIEPAQIES---EIERFRTAQQHVHYELETLR 61 Query: 461 --IDESQVASIRDIFTTHQAMLKDPALREEVQVRLQ-KGLSAEAAWMEEIESAAQQQEAL 517 + + + H +L D L +E ++ + + E A E++E ++ + + Sbjct: 62 ADLAADAPSEMGAFINVHSMILNDAMLVQETFDLIRTRRYNVEWALTEQLERLSRHFDDI 121 Query: 518 HDKLLAERAADLRDVGRRVLACLTGVEAEQAPD-----EPYILVMDEVAPSDVATLNAQR 572 D+ L ER AD+ V RVL L G A + I+V ++AP+D+ Q Sbjct: 122 EDEYLRERKADIEQVVERVLKALAGASVALADGVHGACDEMIVVAHDIAPADMMQFKTQT 181 Query: 573 VAGILTAGGGATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQ 632 G +T GG TSH+AI+AR+LGIPA VG + ++ L+++DG+ G ++V P+ Sbjct: 182 FQGFVTDLGGRTSHTAIVARSLGIPAAVGVQHASALIRQDDLIIVDGDHGIVIVDPAPIV 241 Query: 633 LEQA--RSERAAREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIG 690 LE+ R A E+RK + T G +E+ ANI + A+ GA G+G Sbjct: 242 LEEYSYRQSEKALEQRK--LQRLKFSPTQTLCGTRIELCANIELPDDARAAIDAGATGVG 299 Query: 691 LLRTELVFMNHS-QAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWP----MP 745 L RTE +FMNH + P + Q YRR +E + G P+ +RT+DVG DKPL Sbjct: 300 LFRTEFLFMNHKDRLPEEEEQFGAYRRAVELMNGLPVTIRTIDVGADKPLDSMSGGDGYE 359 Query: 746 AEENPFLGVRGIRLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDR 805 NP LG+R IR SL P + TQLRA+L ++ ++I+ PM+ + E ++ Sbjct: 360 TAANPALGLRAIRWSLSEPQMFLTQLRAILRASAFGSVKILIPMLAHAQEIDQTLDLIRE 419 Query: 806 LRVELPVA------DLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHP 859 + +L A ++QVG MIEIP+AA+ P+ + +DF SIGTNDL QYTLAIDR Sbjct: 420 AKRQLDDAGMAYDPNVQVGAMIEIPAAAIALPLFLKRLDFLSIGTNDLIQYTLAIDRADN 479 Query: 860 TLSGQADGLHPAVLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSAR 919 +++ D LHPAVL LI T+ A G V VCGE+A D LL+G+G+ E S+ Sbjct: 480 SVAHLYDPLHPAVLHLIAFTLREAKRAGVPVSVCGEMAGDPTMTRLLLGMGLTEFSMHPS 539 Query: 920 SIALVKARVRELDFAACQRLAQQALMLPGAHEVRA 954 + +VK V ++ L EV+A Sbjct: 540 QLLVVKQEVLRSHLKTLEKPVADVLASFEPEEVQA 574 Lambda K H 0.317 0.134 0.384 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: 1076 Number of extensions: 45 Number of successful extensions: 6 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: 960 Length of database: 582 Length adjustment: 40 Effective length of query: 920 Effective length of database: 542 Effective search space: 498640 Effective search space used: 498640 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