Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate HSERO_RS00450 HSERO_RS00450 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__HerbieS:HSERO_RS00450 Length = 595 Score = 265 bits (676), Expect = 8e-75 Identities = 193/584 (33%), Positives = 290/584 (49%), Gaps = 29/584 (4%) Query: 277 LRGVCASAGSAFGYVVQVAERTLEMPEF--AADQ-QLERESLERALMHATQALQRLRDNA 333 L G+ S G A G +A L++ + AADQ + E E L+ A+ Q L +R Sbjct: 6 LHGIAVSQGIAIGRAHLMAPAALDVKHYLIAADQVEAEIERLKSAVKAVHQELHTIRSEL 65 Query: 334 AGEAQADI---FKAHQELLEDPSLLEQAQALIAEGK-SAAFAWNSATEATATLFKSLGST 389 EA ++ H +L DP L E Q +I +A +A + E + F + Sbjct: 66 PREAPPELGAFIDVHSLILSDPMLAEVPQDIIRHRYYNAEWALVTQIEELSAQFDEIEDP 125 Query: 390 LLAERALDLMDVGQRVLKLILGV-----PDGVWELPDQAILIAEQLTPSQTAALDTGKVL 444 L ER D+ VG+R+LK++ G P G E I++A ++P+ Sbjct: 126 YLRERKADIQQVGERILKVLTGSATHLPPSG--EAAANIIIVAHDISPADMLQFRESTFA 183 Query: 445 GFATVGGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIE 504 GF T GG SH AI+AR+L +PA G+ + + +++D D G + +DP+ V+ Sbjct: 184 GFVTDLGGPNSHTAIVARSLAIPAAVGMHNASVLVKHDDVLIIDGDAGVVIVDPSPLVLA 243 Query: 505 QLHAKRQQQRQRHQHELENAARA-AVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLR 563 Q A RQ++ R + +L + A+T+DG + AN+ + A GA GIGL R Sbjct: 244 QYRA-RQERLLRERKKLSRLKKTPAITQDGEPITLLANIELPGDAVTAFEAGAMGIGLFR 302 Query: 564 SEFLYQQRS----VAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEA 619 SEFL+ R+ PS DEQ Y A+ R++ +RTLDVG DKPL ++ Sbjct: 303 SEFLFMGRAGHLEKFPSEDEQFEHYKQAVIAM-KGRSVTIRTLDVGADKPLDE-DEETAL 360 Query: 620 NPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPMVSQLSELRLARLMLEEEAL 679 NP LG+R IR CL PQ+ Q RAIL ++ + +++PM++ E+ M+++ Sbjct: 361 NPALGLRAIRYCLSEPQMFLTQLRAILRASAFGPIKLLVPMMAHAFEIDQTLAMIDQAKQ 420 Query: 680 ALGLR------ELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRL 733 L R E+P +G MIE+PAAAL LF +DF SIGTNDL QYTLA+DR + Sbjct: 421 QLRERKQKFDEEIP-VGAMIEIPAAALALPLFVKRLDFLSIGTNDLIQYTLAIDRVDHEV 479 Query: 734 ASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLI 793 A D HP+VL L+++ + G V VCG +A + LLLG+G+ E S+ I Sbjct: 480 AHLYDPLHPAVLFLLSTVISQGRKAGIPVSVCGEMAGDLKWTRLLLGMGLLEFSMHPSQI 539 Query: 794 PAIKAAIREVELSDCQAIAHQVLGLESAEQVREALSVQQQAMVE 837 ++K I +L + +VL + A++ Q E Sbjct: 540 LSVKNEILNSDLRLLEPQVKKVLRATEPAAITAAMTQLQALQAE 583 Lambda K H 0.318 0.132 0.370 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: 1003 Number of extensions: 38 Number of successful extensions: 5 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: 844 Length of database: 595 Length adjustment: 39 Effective length of query: 805 Effective length of database: 556 Effective search space: 447580 Effective search space used: 447580 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