Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate HSERO_RS00450 HSERO_RS00450 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::psRCH2:GFF3291 (960 letters) >FitnessBrowser__HerbieS:HSERO_RS00450 Length = 595 Score = 303 bits (775), Expect = 3e-86 Identities = 200/564 (35%), Positives = 299/564 (53%), Gaps = 26/564 (4%) Query: 404 AGDQVNGIAASPGIAIGPVLVRKPQVID---YPKRGESPVIELQRLDAALDKVHADIGTL 460 A ++GIA S GIAIG + P +D Y + E++RL +A+ VH ++ T+ Sbjct: 2 ASFSLHGIAVSQGIAIGRAHLMAPAALDVKHYLIAADQVEAEIERLKSAVKAVHQELHTI 61 Query: 461 IDE---SQVASIRDIFTTHQAMLKDPALREEVQ-VRLQKGLSAEAAWMEEIESAAQQQEA 516 E + H +L DP L E Q + + +AE A + +IE + Q + Sbjct: 62 RSELPREAPPELGAFIDVHSLILSDPMLAEVPQDIIRHRYYNAEWALVTQIEELSAQFDE 121 Query: 517 LHDKLLAERAADLRDVGRRVLACLTGVEAEQAPDEP----YILVMDEVAPSDVATLNAQR 572 + D L ER AD++ VG R+L LTG P I+V +++P+D+ Sbjct: 122 IEDPYLRERKADIQQVGERILKVLTGSATHLPPSGEAAANIIIVAHDISPADMLQFREST 181 Query: 573 VAGILTAGGGATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQ 632 AG +T GG SH+AI+AR+L IPA VG + + + +L++DG+ G ++V PS Sbjct: 182 FAGFVTDLGGPNSHTAIVARSLAIPAAVGMHNASVLVKHDDVLIIDGDAGVVIVDPSPLV 241 Query: 633 LEQ--ARSERAAREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIG 690 L Q AR ER RE +K + + A+T+DG P+ + ANI G+ A GA GIG Sbjct: 242 LAQYRARQERLLRERKK--LSRLKKTPAITQDGEPITLLANIELPGDAVTAFEAGAMGIG 299 Query: 691 LLRTELVFMNHS----QAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPA 746 L R+E +FM + + P++ Q Y++ + A++GR + +RTLDVG DKPL A Sbjct: 300 LFRSEFLFMGRAGHLEKFPSEDEQFEHYKQAVIAMKGRSVTIRTLDVGADKPLDEDEETA 359 Query: 747 EENPFLGVRGIRLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDRL 806 NP LG+R IR L P + TQLRA+L ++ P++++ PM+ + E AM+D+ Sbjct: 360 L-NPALGLRAIRYCLSEPQMFLTQLRAILRASAFGPIKLLVPMMAHAFEIDQTLAMIDQA 418 Query: 807 RVELPVA------DLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPT 860 + +L ++ VG MIEIP+AAL P+ + +DF SIGTNDL QYTLAIDR Sbjct: 419 KQQLRERKQKFDEEIPVGAMIEIPAAALALPLFVKRLDFLSIGTNDLIQYTLAIDRVDHE 478 Query: 861 LSGQADGLHPAVLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARS 920 ++ D LHPAVL L+ + G V VCGE+A D LL+G+G+ E S+ Sbjct: 479 VAHLYDPLHPAVLFLLSTVISQGRKAGIPVSVCGEMAGDLKWTRLLLGMGLLEFSMHPSQ 538 Query: 921 IALVKARVRELDFAACQRLAQQAL 944 I VK + D + ++ L Sbjct: 539 ILSVKNEILNSDLRLLEPQVKKVL 562 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: 1160 Number of extensions: 55 Number of successful extensions: 7 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: 595 Length adjustment: 40 Effective length of query: 920 Effective length of database: 555 Effective search space: 510600 Effective search space used: 510600 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