Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate AZOBR_RS18900 AZOBR_RS18900 peptidase
Query= reanno::psRCH2:GFF3291 (960 letters) >FitnessBrowser__azobra:AZOBR_RS18900 Length = 766 Score = 322 bits (826), Expect = 5e-92 Identities = 217/605 (35%), Positives = 323/605 (53%), Gaps = 28/605 (4%) Query: 373 VEPLPAPGEASEPPVTAQGPAESAIDQAALRAGDQVNGIAASPGIAIGPVLVRKPQVIDY 432 V L A GE P A S D A L A +++G + + G+A+G ++ +PQ+ Sbjct: 168 VAELVAQGELVNPQEVA-----STGDPALLPA--RLSGTSLASGLAMGLAVIHRPQLTIR 220 Query: 433 PKRGESPVIELQRLDAALDKVHADIGTLIDESQVASI---RDIFTTHQAMLKDPALREEV 489 E EL RL+AA+ +H+ I L++ + +A + +DI T++ +D + Sbjct: 221 QMVSEDAESELARLNAAIATMHSAIDDLLNAAALAGLSEPKDILETYRMFAEDRGWLSRI 280 Query: 490 QVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLAERAADLRDVGRRVLACLTGVEAEQ-- 547 + ++ GL+AE A + + L D + ER DL D+ R+L L G ++E Sbjct: 281 REAIRMGLTAEGAVQQVQNDTRARMSHLTDPYIRERLLDLEDLTNRLLQHLAGRKSEADG 340 Query: 548 -APDEPYILVMDEVAPSDVATLNAQRVAGILTAGGGATSHSAIIARALGIPAIVGAGPGV 606 E +LV + P+++ + +R+ G++ G +SH I+ARAL IP +V A + Sbjct: 341 GTLPEDIVLVARSMGPAELLDYDQRRLRGVILEEGSPSSHVCIVARALNIP-VVQAPDAL 399 Query: 607 LGLARNTLLLLDGERGELLVAPSGAQLEQARSERAAREERKHLANER-RMDAAVTRDGHP 665 + +++DG+ G+ V P+ ++ A +E A RK E R +VTRDG P Sbjct: 400 NRIEPLDPVIVDGDHGQAFVRPA-EDIQMAFAEAVALRARKEQMYEAIRAQPSVTRDGVP 458 Query: 666 VEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHSQAPNQATQEAEYRRVLEALEGRP 725 + I N G + P A GAEGIGL RTE+ FM S P+ Q Y R+L+ + +P Sbjct: 459 ISIQLNCGLLIDLPHLKASGAEGIGLYRTEIPFMVRSTYPDVHAQTDLYSRILDQTDDKP 518 Query: 726 LVVRTLDVGGDKPLPYWPMP-AEENPFLGVRGIRLSLQRPDILETQLRALLASADGRPLR 784 +V RTLDVGGDK LPY EENP LG R IR+ L P +L QLRALL ++ GRPL Sbjct: 519 VVFRTLDVGGDKMLPYIAASEGEENPALGWRAIRIGLDHPSLLRQQLRALLRASAGRPLS 578 Query: 785 IMFPMVGNIDEWRTAKAMVD----RLRVE--LPVADLQVGIMIEIPSAALIAPVLAQEVD 838 +MFPM+ + E+ A+ ++D RL+ + P + ++VG MIE+P+ P L VD Sbjct: 579 VMFPMIAEVAEFDAARRLLDLEINRLKGQGGEPPSRVRVGTMIEVPALLWQLPALLPRVD 638 Query: 839 FFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLIGMTVEAAHAHGKWVGVCGELAA 898 F S+G+NDLTQY A DRG+P SG+ D L PA++ L+ VEA G V +CGE+A Sbjct: 639 FLSVGSNDLTQYIFASDRGNPRTSGRYDPLSPAMMSLLRRLVEACGDAGVPVSICGEMAG 698 Query: 899 DALAVPLLVGLGVDELSVSARSIALVKARVRELDFAACQRLAQQALMLPGAH----EVRA 954 L L+G+G LS+S S+ VK +R LD A R L L G H ++R+ Sbjct: 699 RPLDAMALIGIGFRTLSMSPPSVGPVKTMLRSLDVAVL-RQYMNGLYLRGDHSLRDKLRS 757 Query: 955 FVGEH 959 F +H Sbjct: 758 FAKDH 762 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: 1578 Number of extensions: 76 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: 766 Length adjustment: 42 Effective length of query: 918 Effective length of database: 724 Effective search space: 664632 Effective search space used: 664632 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: 56 (26.2 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