Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate WP_043743857.1 AMB_RS08150 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1146 (953 letters) >NCBI__GCF_000009985.1:WP_043743857.1 Length = 757 Score = 324 bits (830), Expect = 2e-92 Identities = 200/579 (34%), Positives = 307/579 (53%), Gaps = 22/579 (3%) Query: 371 EEVEPLPAVSQHREVIADVAEVL----LAPASGSLI-----QAIAAAPGIAIGPAHIQVQ 421 EE+E L V+ + E++ L P G+ + + + G+ +G A + Sbjct: 146 EEIETLETVAMVLAELLVSGELVNRAELVPVDGNALLPLRMEGVKLNGGVGVGVAVLHRP 205 Query: 422 QVIDYPLRGESAAIERERLKQALADVRRDIEGLIERSKAK--AIREIFITHQEMLDDPEL 479 ++ L E E ERLK+AL ++ +E L R + + R++ T++ +D Sbjct: 206 RITIQRLVAEDTDAELERLKKALTGIKLALEELFSRPEMRDGEHRDVLETYRMFAEDKGW 265 Query: 480 TDEVDTRLKQGESAEAAWMAVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLSGVET 539 + + + G +AEAA V + + + D L ER D D+ R+L L+G + Sbjct: 266 LNRISEAIHTGLTAEAAVQKVHDDTRARMSQITDPYLRERMHDFEDLANRLLQHLAGGDD 325 Query: 540 PAEP-----EQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALV 594 P + IL+ +GP ++ DP R+ G++ G AT+H AIVARAL IP + Sbjct: 326 DQRPGAADLPEGAILIGRNLGPMELFDYDPKRLRGLVLEEGSATSHVAIVARALDIPVVG 385 Query: 595 GAGAAVLLLKPGTPLLIDGQRGRLHVDADAATLQRATEERDTRELRLKAAAEQRHQPALT 654 + ++P P++ DG G++ + + + R+LR A R PA+T Sbjct: 386 RVKDVLDKIEPLDPVICDGDNGQVFIRPPDDIRETYIDAISQRQLRQAVYARLRELPAVT 445 Query: 655 TDGHAVEVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHSQAPDEATQEVEYRRVLDG 714 + + N G + + GA+GIGL RTEL FMA S PD A Q + Y+++LD Sbjct: 446 RQDVRIGIHMNAGLLLDLQHLHDSGADGIGLYRTELPFMARSSLPDVAAQTLLYKKILDQ 505 Query: 715 LAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQVMEAQLRALLRAADN 774 G+P+V RTLDVGGDK LPYW +E+NP LG R IR+TL RP VM +QLRALLRAA Sbjct: 506 AEGKPVVFRTLDVGGDKVLPYWNPYEEDNPALGWRSIRITLDRPAVMRSQLRALLRAAQG 565 Query: 775 RPLRIMFPMVGSVDEWRQARDMTER-LRLEIPVAD-----LQLGIMIEVPSAALLAPVLA 828 R L +MFPM+ V E+ QAR + ++ L E + + L++G M+EVP+ AL L Sbjct: 566 RELSVMFPMIAEVSEFVQARLILDKELERERAMGNPMPSRLKVGTMLEVPALALQLDALL 625 Query: 829 KEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCG 888 VDF S+G+NDLTQ+ A+DRG+P ++ + D L PA+++ + +G + VCG Sbjct: 626 PMVDFVSIGSNDLTQFLFAVDRGNPRIAERYDSLAPAMVRFMRYVAAKCAQYGVTLSVCG 685 Query: 889 ELAADPLAVPVLVGLGVDELSVSGRSIAEVKARIRELSL 927 E+A PL L+G+G+ LS+S +I VK +R L + Sbjct: 686 EMAGRPLEAMALIGVGIRHLSLSAPNIGPVKTMVRSLDI 724 Lambda K H 0.318 0.135 0.381 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: 1340 Number of extensions: 60 Number of successful extensions: 3 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: 953 Length of database: 757 Length adjustment: 42 Effective length of query: 911 Effective length of database: 715 Effective search space: 651365 Effective search space used: 651365 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