Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Pf6N2E2_5969 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5969 Length = 514 Score = 350 bits (899), Expect = e-101 Identities = 212/485 (43%), Positives = 290/485 (59%), Gaps = 13/485 (2%) Query: 14 LALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHI 73 L I K+FPGV+AL + A+ G+VHALMGENGAGKSTL+KIL GAY G+ I Sbjct: 16 LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPS-SGDLQI 74 Query: 74 DGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAP 133 Q + G + GVAVI+QEL L P ++VAEN++LG R GLV RG + + Sbjct: 75 GEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALT 134 Query: 134 TLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALI 193 L L + P V LS+ QRQLVEIA+A+ A ++ DEPT+ LS E DRL A+I Sbjct: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 Query: 194 RQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDR-AHLSQAALVKMMVGRDLS 252 +LR EG +LY+SHRM E+ + + VTV +DG +V T + + L+ LV MVGRD+ Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254 Query: 253 GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFG 312 Y + +V L V+ + + SF + GE+LGL GLVGAGRTEL RL+ G Sbjct: 255 DIY--DYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSG 312 Query: 313 ADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINL 372 + + G + + + L PR AI AG+ EDRK +G+ SV ENIN Sbjct: 313 LERQREGSLVLHDK-------ELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENIN- 364 Query: 373 IVAARDALGLGRLNR-TAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431 I A LG L R R + I +L ++ A + LSGGNQQK +L R L + Sbjct: 365 ISARPSHSTLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSM 424 Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491 +VL+LDEPTRG+DIGAK+EIY++I+ LA G+A++++SS+L EV+G+ DR+LV+ EG Sbjct: 425 PMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGA 484 Query: 492 LAGEV 496 + GE+ Sbjct: 485 MRGEL 489 Score = 74.7 bits (182), Expect = 8e-18 Identities = 56/225 (24%), Positives = 107/225 (47%), Gaps = 8/225 (3%) Query: 32 VELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARDLGV 91 V + GE+ L G GAG++ L+++LSG G + + +++ P+ A GV Sbjct: 283 VSFQVHKGEILGLFGLVGAGRTELLRLLSGL-ERQREGSLVLHDKELKLRSPRDAIAAGV 341 Query: 92 AVIYQELS---LAPNLSVAENIYLGRALQRR--GLVARGDMVRACAPTLARLGADFSPAA 146 + ++ + P SV ENI + G + RGD R A + +P A Sbjct: 342 LLCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWERGNADKQIKSLKVKTPTA 401 Query: 147 N--VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMAIL 204 + LS +Q + R + ++L++DEPT + ++ +I L +G+A++ Sbjct: 402 GQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVI 461 Query: 205 YISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249 +S + E+ ++DR+ VL +G G L R +++ L+++ + R Sbjct: 462 VVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPR 506 Lambda K H 0.320 0.136 0.382 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: 631 Number of extensions: 34 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 540 Length of database: 514 Length adjustment: 35 Effective length of query: 505 Effective length of database: 479 Effective search space: 241895 Effective search space used: 241895 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 (21.8 bits) S2: 52 (24.6 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