Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate AO356_17540 AO356_17540 PTS N-acetyl-D-glucosamine transporter
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_17540 Length = 837 Score = 640 bits (1650), Expect = 0.0 Identities = 370/831 (44%), Positives = 509/831 (61%), Gaps = 17/831 (2%) Query: 7 LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66 L L APLSG +L L VPD VF+S +GDG+ IDP + TL AP + ++ +GHAV++ Sbjct: 8 LILSAPLSGPVLTLANVPDAVFASGAMGDGIAIDPLNDTLYAPCDAEVIHVARTGHAVTL 67 Query: 67 TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126 DNG ++L+H+GLDTV L G+GF+ LV+EG RV GQPL+ +D D VAL +SL++L++ Sbjct: 68 RADNGAELLLHLGLDTVELQGEGFSMLVKEGARVSHGQPLLRYDVDKVALRCKSLVSLLV 127 Query: 127 VVSGEPFSLLADGL--VETGQPLLQLSPS--GAVEAVDEEEGDALFSKPLTLPNANGLHA 182 + +GE F L V+ G+PLL + G E D++ G +F + + + + GLHA Sbjct: 128 ITNGEHFQARPITLKGVKVGEPLLHILAKAVGQAEHHDQDSGIEVFGQ-VRIAHRGGLHA 186 Query: 183 RPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKA 242 RPAA+ Q A+GF + LH +SA+ S++ +M L + + VS G DAEAA++A Sbjct: 187 RPAALVRQTAQGFKSRSQLHFSGKSASCDSVMGMMGLAITEQAQVHVSCRGSDAEAALQA 246 Query: 243 LVALLAEGCGE---AVVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQG 299 L+ L+ E A EP + +L GVCA+PG G +V+++ +L G Sbjct: 247 LLTTLSTALVEEAHASAPPPEPPRANAEEGVLHGVCAAPGLVTGPLVRLSGIQLPEDIGG 306 Query: 300 TGGATERAALTRGLLAANEALQVLQDKAAGSAQAE---IFRAHQELLEDPTLLEHAHRLL 356 +R L+ L + + + A + IF AH LLEDP LL+ A + Sbjct: 307 HAIEEQRQRLSDALAQVRGEIHLTLEHARARQHRDEEAIFSAHLALLEDPVLLDAADLFI 366 Query: 357 GEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAW--DLP 414 +G +A AW+ + + Q LG+ L+AERA DL D+ QRVL+++LG AW D+ Sbjct: 367 EQGSAAPHAWSRSIDTQCQVLQQLGSTLLAERANDLRDLRQRVLRVLLG---EAWQFDVA 423 Query: 415 ERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALA 474 AI+ A++LTPS L + V G V GGATSHVAILAR GLP + + ++LA Sbjct: 424 AGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCLVALGDELLAQE 483 Query: 475 NGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTA 534 G+ V+LDAD G L L P + + Q+ A+ + + + A PA T DG VEV A Sbjct: 484 QGQAVVLDADGGRLELTPTVERLAQVRQAQTRRTALRAQQQSLAHTPARTVDGVEVEVAA 543 Query: 535 NVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVR 594 NVAS E +L G +GVGLLR+EFL++DR+ AP EEQ Y A+ A+G ++ +++R Sbjct: 544 NVASSAEAGESLANGADGVGLLRTEFLFVDRHTAPDEEEQRQAYQAVLEAMG-DKPVIIR 602 Query: 595 TLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPM 654 T+DVGGDK L Y+P+ +E NP LGLRGIRL RP LL +Q RA+L + R I+LPM Sbjct: 603 TIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQVRPDLLDQQLRALLQTRPLDRCRILLPM 662 Query: 655 VSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLT 714 V+ + EL RK L+ LGL+E P+LG+M+EVP+AAL+A+ A H DF SIGTNDL+ Sbjct: 663 VTEVDELLHIRKRLDALGSELGLSERPQLGVMVEVPAAALLAEQLAEHADFLSIGTNDLS 722 Query: 715 QYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIG 774 QYTLAMDRDH LA + D+ HPA+LRLIA T A HG+WVGVCGALAS+ LA PVLIG Sbjct: 723 QYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVLIG 782 Query: 775 LGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQY 825 LGV ELSVS P I IK VR LD A C ++ ++L L A VR A ++ Sbjct: 783 LGVRELSVSPPQIGEIKDRVRHLDAAQCARLSNELLNLGSALAVRRACHRH 833 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: 1571 Number of extensions: 73 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: 837 Length adjustment: 42 Effective length of query: 796 Effective length of database: 795 Effective search space: 632820 Effective search space used: 632820 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