Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 Length = 514 Score = 350 bits (897), Expect = e-100 Identities = 209/484 (43%), Positives = 283/484 (58%), Gaps = 11/484 (2%) Query: 14 LALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHI 73 L I KTFPGV+AL + A+ G+VHALMGENGAGKSTL+KIL GAYT G+ I Sbjct: 16 LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPS-SGDLQI 74 Query: 74 DGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAP 133 Q+ + GVAVI+QEL L P ++VAEN++LG GL+ RG + + Sbjct: 75 GEQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRGVLRQQALA 134 Query: 134 TLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALI 193 L L + P V LS+ QRQLVEIA+A+ A ++ DEPT+ LS E DRL A+I Sbjct: 135 CLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 Query: 194 RQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTL-DRAHLSQAALVKMMVGRDLS 252 +LR EG +LY+SHRM E+ + + VTV +DG FV T D + L+ LV MVGRD+ Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDIQ 254 Query: 253 GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFG 312 Y + V L V + + SF+ GE+LGL GLVGAGRTEL R++ G Sbjct: 255 DIY--DYRSRPRGAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRMLSG 312 Query: 313 ADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINL 372 T G + + L PR AI AGI EDRK +G+ SV ENIN+ Sbjct: 313 LTRNTAGRLELRGR-------ELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINI 365 Query: 373 IVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQ 432 + L + + I L ++ +A + LSGGNQQK +L R L + Sbjct: 366 SARGAHSTFGCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMP 425 Query: 433 PRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTL 492 +VL+LDEPTRG+DIGAK+EIY++I+ LA SG+A++++SS+L EV+G+ DR+LV+ EG + Sbjct: 426 MKVLLLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAM 485 Query: 493 AGEV 496 GE+ Sbjct: 486 RGEL 489 Score = 81.3 bits (199), Expect = 8e-20 Identities = 61/233 (26%), Positives = 114/233 (48%), Gaps = 10/233 (4%) Query: 24 PGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGP 83 PG+R V A+ GE+ L G GAG++ L ++LSG T + G + G+ +++ P Sbjct: 277 PGLR--EPVSFEAHKGEILGLFGLVGAGRTELFRMLSGL-TRNTAGRLELRGRELKLHSP 333 Query: 84 QSARDLGVAVIYQELS---LAPNLSVAENIYLGR--ALQRRGLVARGDMVRACAPTLARL 138 + A G+ + ++ + P SVAENI + A G + RG + A + Sbjct: 334 RDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNADKQIKA 393 Query: 139 GADFSP--AANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 196 +P A + LS +Q + R + ++L++DEPT + ++ +I L Sbjct: 394 LKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNL 453 Query: 197 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249 G+A++ +S + E+ ++DR+ VL +G G L R +++ L+++ + R Sbjct: 454 AASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQANESNLLQLALPR 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: 615 Number of extensions: 35 Number of successful extensions: 9 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 Apr 09 2024. 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