Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate AO353_04460 AO353_04460 PTS N-acetyl-D-glucosamine transporter
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04460 Length = 838 Score = 661 bits (1706), Expect = 0.0 Identities = 385/831 (46%), Positives = 522/831 (62%), Gaps = 16/831 (1%) Query: 7 LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66 L L APLSG +L L KVPDPVF+S +GDG+ IDP + TL AP AGV+ ++ +GHAV++ Sbjct: 8 LTLSAPLSGPVLTLAKVPDPVFASGAMGDGIAIDPLNNTLHAPCAGVVVHVARTGHAVTL 67 Query: 67 TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126 DNG ++L+H+GLDTV L G+GF+ LV+EG RV GQ L+ FD D VA +SL++L++ Sbjct: 68 RADNGAELLLHLGLDTVELQGEGFSMLVKEGTRVSNGQALLRFDLDQVAQGCKSLVSLLV 127 Query: 127 VVSGEPFSLLADGL--VETGQPLLQLSPSGAVEA-VDEEEGDALFSKPLTLPNANGLHAR 183 + + E F +L L V+ G+PLL + P A V+ + A + + + GLHAR Sbjct: 128 LTNSEDFQVLPITLKSVKVGEPLLHIVPRTTHSAQVEADSSGAEVHGHIRIIHRGGLHAR 187 Query: 184 PAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKAL 243 PAA+ Q A FN+ LH +SA+ SL+ +M L + D +QVS G DA+AA++AL Sbjct: 188 PAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDEVQVSCKGADAKAALQAL 247 Query: 244 VALLAEGCGE-----AVVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQ 298 + L+ + A +A+ T + A +L GVCA+PG G + Q+ L + Sbjct: 248 LNALSTAVNDDSHAAAPTPIAQRTRT-AEAGVLNGVCAAPGLVGGPLFQLAAIPLP-EDT 305 Query: 299 GTGGATERA-ALTRGL-LAANEALQVLQD--KAAGSAQAEIFRAHQELLEDPTLLEHAHR 354 G A E+ AL R L +E + L K + + +IF AH LLEDP LLE A + Sbjct: 306 GKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDPALLEAAIQ 365 Query: 355 LLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLP 414 + +G +A AW+ + A + Q LGN L+AERA DL D+ QRVL+ +LG QD +D+P Sbjct: 366 SIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLG-QDWHYDVP 424 Query: 415 ERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALA 474 AI+ A +LTPS L + V G GGATSHVAILAR GLP + + A +L Sbjct: 425 AGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLVALSASLLQQP 484 Query: 475 NGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTA 534 G+ V+LDAD G L L P+ +EQ+ A++ + R +R AQA PA TRDG +EV A Sbjct: 485 QGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHTRDGLRIEVAA 544 Query: 535 NVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVR 594 NVAS E AL G +GVGLLR+EFL++DR AP +EQ Y A+ A+G ++++++R Sbjct: 545 NVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDAMG-DKSVIIR 603 Query: 595 TLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPM 654 T+DVGGDK L Y+P+ AE NP LGLRGIR+ RP+LL +Q RA+L + R I+LPM Sbjct: 604 TIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLQRCRILLPM 663 Query: 655 VSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLT 714 V+ + EL R+ L+ L LT+ +LG+MIEVP+AAL+A+ A H DF SIGTNDL+ Sbjct: 664 VTEVDELLYIRQRLDALCAELALTQRLELGVMIEVPAAALLAEQLAEHADFLSIGTNDLS 723 Query: 715 QYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIG 774 QYTLAMDRDH LA + D+ HPA+LRLIA T A H +WVGVCGALAS+ LA PVLIG Sbjct: 724 QYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVCGALASDPLATPVLIG 783 Query: 775 LGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQY 825 LG+ ELSVS P + IK VR+LD ADC+ + +L L A VR A Q+ Sbjct: 784 LGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLSSATAVRHACHQH 834 Lambda K H 0.318 0.133 0.371 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: 1530 Number of extensions: 68 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: 838 Length of database: 838 Length adjustment: 42 Effective length of query: 796 Effective length of database: 796 Effective search space: 633616 Effective search space used: 633616 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