Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate PfGW456L13_4832 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
Query= reanno::pseudo3_N2E3:AO353_05485 (953 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4832 Length = 838 Score = 452 bits (1163), Expect = e-131 Identities = 275/678 (40%), Positives = 378/678 (55%), Gaps = 22/678 (3%) Query: 277 ELPADWPSARIALANAHGLHARPAKILAQLAKSFEGEIRIRIVDGQDSAVSVKSLSKLLS 336 EL + I +A+ GLHARPA ++ Q A+ F+ + ++ + + SL L+ Sbjct: 166 ELAGEEVVGHIRIAHRGGLHARPAALIRQTAQGFKSKSQLHFAG---KSATCDSLIGLMG 222 Query: 337 LGARRGQVLELIAEPSIAADALPALLRAIEEGLGEDIEPL-PTVSAQSEVIDEITDVVVA 395 L +++ + A AL ALL A+ L ED PT AQ Sbjct: 223 LAIGEQAEVQVSCQGPDAEAALQALLTALSTALAEDSHAAAPTTIAQRN----------R 272 Query: 396 PASGCVIQAVAAAPGIAIGPAHIQVLQAIDYPLRG--ESTAIERERLKTSLADVRRDIEG 453 PA V+ V AAPG+ GP + L AI P+ +++ L +L+ VR +IE Sbjct: 273 PAEAGVLHGVCAAPGLVGGP--LFHLNAISLPVDAGHHDPQQQQQVLDAALSQVRSEIER 330 Query: 454 ---LIQRSKAKAIREIFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIDAAARQQES 510 L ++ K A IF H +L+DP L D + QG +A AW ID + Sbjct: 331 TLVLAKKHKDTAEEAIFAAHLALLEDPALLDAAIQTVAQGTAATHAWSQAIDVQCEVLQQ 390 Query: 511 LQDALLAERAADLRDIGRRVLAQLCGIETPSEPDQPYILVMDEVGPSDVARLDPTRVAGI 570 LLAERA DLRD+ +RVL L G + I+ E+ PSD+ +L VAG+ Sbjct: 391 TGSTLLAERANDLRDLKQRVLRALLGDTWHYDVPAGAIVAAHELTPSDLLQLSQQGVAGL 450 Query: 571 LTARGGATAHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRA 630 A GGAT+H AI+AR G+P +V G+ +L G P++LD GRL + A L Sbjct: 451 CMAEGGATSHVAILARGKGLPCMVALGSTLLDQQQGQPVVLDADGGRLELTPSAERLADV 510 Query: 631 AEERDNREQRLQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGAEGIGLLRTEL 690 + + ++QR AQ H PALTTDG +EV AN+ S A+ GA+G+GLLRTE Sbjct: 511 RQLQQQQQQRRAEQQAQAHTPALTTDGLRIEVAANVASSTEAADALANGADGVGLLRTEF 570 Query: 691 IFMAHQQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRG 750 +F+ APDE Q Y+ VLD + + +++RT+DVGGDK L Y P+ E NP LG+RG Sbjct: 571 LFVDRHTAPDEQEQHHAYQAVLDAMGDKSVIIRTIDVGGDKQLDYLPLPAEANPVLGLRG 630 Query: 751 IRLTLQRPQIMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDMTERLRLEIPVADL- 809 IRL RP++++ QLRALL RI+ PMV VDE + L E+ +A Sbjct: 631 IRLAQARPELLDQQLRALLHLRPLSRCRILLPMVTEVDELLHIHQRLDALCGELGLAQRP 690 Query: 810 QLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQL 869 +LG+MIEVP+AALLA LA+ DF S+GTNDL+QYTLA+DR H L+A+ D LHPA+L+L Sbjct: 691 ELGVMIEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRL 750 Query: 870 IDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIGEVKARVRELSLAQ 929 I T A H +WVGVCG LA+DPLA PVL+GLGV ELSVS +GE+K RVR L ++ Sbjct: 751 IAQTCAGAAQHNRWVGVCGALASDPLATPVLIGLGVSELSVSPVQVGEIKDRVRHLDASE 810 Query: 930 VKHLAQLALAVGSANEVR 947 + ++Q L + SA+ VR Sbjct: 811 CRRISQGLLKLSSASAVR 828 Lambda K H 0.319 0.135 0.383 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: 1636 Number of extensions: 80 Number of successful extensions: 6 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: 838 Length adjustment: 43 Effective length of query: 910 Effective length of database: 795 Effective search space: 723450 Effective search space used: 723450 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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