Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate 3608669 Dshi_2062 PTSINtr with GAF domain, PtsP (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_1146 (953 letters) >FitnessBrowser__Dino:3608669 Length = 747 Score = 264 bits (674), Expect = 2e-74 Identities = 188/566 (33%), Positives = 285/566 (50%), Gaps = 17/566 (3%) Query: 401 LIQAIAAAPGIAIGPAHIQVQQVIDYPLRGESAAIERERLKQALADVRRDIEGLIE---R 457 +I+ A GIA G ++ +V+ L + E RL+ A+ +R ++ +++ + Sbjct: 182 MIRGGVAQEGIAKGHVYLHEPRVVVTKLVSDDPEAELVRLRGAVDQLRVSVDEMLDIAPK 241 Query: 458 SKAKAIREIFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIEAAAKQQESLQDALLA 517 A+ + +I ++ + ++ + G SAEAA AA + E + DA L Sbjct: 242 GDAEQL-QILEAYRMFANSRGWMRRMEESIDSGLSAEAAVEKEQSAARSRMERVPDAYLR 300 Query: 518 ERAADLRDIGRRVLAQLSGV--ETPAEPEQPYILVMDEVGPSDVARLDPTR-VAGILTAR 574 ER DL D+ R+L L+G ET AE ILV +GP ++ LD R + GI+ Sbjct: 301 ERLHDLDDLSNRLLRLLTGQGGETGAEIPADPILVARNIGPGEL--LDYGRALKGIILEE 358 Query: 575 GGATAHSAIVARALGIPALVGAGAAVLLLKPGTPLLIDGQRGRLHVDADAATLQRATEER 634 G +H+AIVARAL IP +V A G +L+DG++G +H+ D L T++ Sbjct: 359 GSVGSHAAIVARALAIPLIVHAKRITTEALNGDLVLVDGEQGIVHLRPDDRVLAHFTDKI 418 Query: 635 DTRELRLKAAAEQRHQPALTTDGHAVEVFANIGESAGVTSAVEQGAEGIGLLRTELIFMA 694 + + A R +PA T G + + N G A + S GAEG+GL RTEL F+ Sbjct: 419 AMQAKAQERYASIRDKPAETLCGSVISLTMNAGLMADLPSLPSSGAEGVGLFRTELQFLT 478 Query: 695 HSQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLT 754 S+ P + Y RVLD G+ +V RTLD+G DK LPY E NP LG R IR+ Sbjct: 479 RSKVPRRSELAEIYARVLDAADGKRVVFRTLDIGSDKVLPYMKPQDEPNPALGWRAIRVG 538 Query: 755 LQRPQVMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDMTER-------LRLEIPVA 807 L +P VM QL+AL+R A+ RPL +MFP + ++E+ +ARD R L +P Sbjct: 539 LDKPGVMRMQLQALIRGANGRPLTVMFPFIAQLEEFTRARDALLREIDREAALGRTLP-E 597 Query: 808 DLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVL 867 +++G M+E PS A + DF S+G NDL Q+ A DR + + + D L+ + L Sbjct: 598 SVEIGAMLETPSLAFAPNSFFEMADFVSIGGNDLKQFFFAADRENERVRRRYDTLNVSFL 657 Query: 868 QLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSGRSIAEVKARIRELSL 927 LI++ V G + CGE A P+ +G+ LS+ SI VK +R L Sbjct: 658 SLIELIVSRCRDVGTPLSFCGEDAGRPIEALCFAAMGLRSLSMRPASIGPVKHLLRRSDL 717 Query: 928 TQTQTLAQQALAVGSANEVRALVEAL 953 + + + QA A G+ A++E L Sbjct: 718 REARAVITQARASGAMTVRPAVMEWL 743 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: 1313 Number of extensions: 77 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 953 Length of database: 747 Length adjustment: 42 Effective length of query: 911 Effective length of database: 705 Effective search space: 642255 Effective search space used: 642255 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