Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 381 bits (979), Expect = e-110 Identities = 227/508 (44%), Positives = 307/508 (60%), Gaps = 16/508 (3%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 PL +R ICK FPGV+AL V Y GEVH L+GENGAGKS+LMK+L G Y AD GE Sbjct: 9 PLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVAD-AGEF 67 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR--GLVARGDMVR 129 + DG V I P LG+AVI+QE SL P L +A+NI+LGR + R G V M Sbjct: 68 YHDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHA 127 Query: 130 ACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRL 189 L LG + S V L +AQ+Q+VEIA+A+ ARILV+DEPT LS ET++L Sbjct: 128 EARRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKL 187 Query: 190 FALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249 FA+I +L+ +G++++YISHRMAE+ L DR+T+LRDG VG + LV MVGR Sbjct: 188 FAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVGR 247 Query: 250 DLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARL 309 + Y++ A EV L VR+V+ + + +RAGE++GLAGLVG+GR+E+AR Sbjct: 248 KVDMSYSRER-SAQPGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVARA 306 Query: 310 VFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHEN 369 VFGAD +GE+ I G +T GGP +A + G A + E RK +GL L ++V +N Sbjct: 307 VFGADPIRQGEIYI-----FGKRLT---GGPDRARELGAALIPESRKSEGLALIRTVRDN 358 Query: 370 INLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLL 429 + L+ R A A I L I LSGGNQQK+++ + L Sbjct: 359 L-LLAGLRRAFPARWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWL 417 Query: 430 EIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMRE 489 + ++ I DEPTRG+D+GAK+EI+ LI++L + G +L+ISSELPE++ +CDR VMR Sbjct: 418 VAEAKLFIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRG 477 Query: 490 GTLAGEVRPAGSAAETQERIIALATGAA 517 G +AGEV A T+ERI+ L A Sbjct: 478 GRIAGEV---AHAEMTEERILQLGMNDA 502 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: 700 Number of extensions: 45 Number of successful extensions: 11 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: 540 Length of database: 502 Length adjustment: 35 Effective length of query: 505 Effective length of database: 467 Effective search space: 235835 Effective search space used: 235835 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