Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 348 bits (894), Expect = e-100 Identities = 217/510 (42%), Positives = 302/510 (59%), Gaps = 17/510 (3%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPD-SGRVMI 63 L NI K FPGVRAL V G+VH LMGENGAGKSTL+KIL G Y D G I Sbjct: 11 LALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHI 70 Query: 64 DGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRE 123 DG V+ S+ G+AVI+QEL P+L+VAEN+ LG+ G V + + R Sbjct: 71 DGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAP 130 Query: 124 RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLV 183 L +G P A + LSIAQRQ+VEI +A+ AR++ +DEPT+ LS ET+ LF L+ Sbjct: 131 TLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALI 190 Query: 184 RDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREIS 243 R LR + A++YISHRM EI EL D T+ RDG + + +++ +V MVGR++S Sbjct: 191 RQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAH-LSQAALVKMMVGRDLS 249 Query: 244 DIY--NYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYG 301 Y + EV + + + + SF++R GE++G GLVGAGR+EL LV+G Sbjct: 250 GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFG 309 Query: 302 ADHKKGGELLL-----DGKPIKVRSAG--EAIRHGIVLCPEDRKEEGIVAMATVSENIN- 353 AD + GE+ + G + + + G +AI GI EDRK +G+ +V ENIN Sbjct: 310 ADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINL 369 Query: 354 ISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAE 413 I R L +G L+R I L I+ + + LSGGNQQK +LSR L E Sbjct: 370 IVAARDALGLGR-LNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSR-LLE 427 Query: 414 PDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQG 473 +V+ILDEPTRG+D+GAK EIY +I LA+ G AI+MISSELPEV+G+ DR++VMR+G Sbjct: 428 IQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREG 487 Query: 474 RISGELTRKDA---TEQSVLSLALPQSSTA 500 ++GE+ + T++ +++LA ++ A Sbjct: 488 TLAGEVRPAGSAAETQERIIALATGAAAAA 517 Score = 65.9 bits (159), Expect = 4e-15 Identities = 59/242 (24%), Positives = 108/242 (44%), Gaps = 9/242 (3%) Query: 252 PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGA-DHKKGGEL 310 PL +R K G + GE+ G GAG+S LM ++ GA GGE Sbjct: 9 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 68 Query: 311 LLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRK 370 +DG+ +++ A G+ + +E + +V+ENI + R R G+ Sbjct: 69 HIDGQRVQIDGPQSARDLGVAVI---YQELSLAPNLSVAENIYLG--RALQRRGLVARGD 123 Query: 371 KEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDV 430 A +L +P+ + LS +Q ++R + +++++DEPT + Sbjct: 124 MVRACAPTLARLGADFSPA--ANVASLSIAQRQLVEIAR-AVHFEARILVMDEPTTPLST 180 Query: 431 GAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVL 490 ++ +I QL G AI+ IS + E+ ++DR+ V+R G G L R ++ +++ Sbjct: 181 HETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALV 240 Query: 491 SL 492 + Sbjct: 241 KM 242 Lambda K H 0.320 0.136 0.385 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: 681 Number of extensions: 36 Number of successful extensions: 11 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: 512 Length of database: 537 Length adjustment: 35 Effective length of query: 477 Effective length of database: 502 Effective search space: 239454 Effective search space used: 239454 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