Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate BPHYT_RS16930 BPHYT_RS16930 arabinose ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__BFirm:BPHYT_RS16930 Length = 512 Score = 418 bits (1074), Expect = e-121 Identities = 224/498 (44%), Positives = 333/498 (66%), Gaps = 13/498 (2%) Query: 1 MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60 M L +I K FPGV AL GVS + G+VH ++GENGAGKSTL+KI+ G YQPD G Sbjct: 1 MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60 Query: 61 IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120 ++ +G VR+ + +I AGI + QEL + +L+VAEN+ +G +++ RE Sbjct: 61 VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVN----KRE 116 Query: 121 AEKFMKEE---FGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKET 177 A++F++E G+ +DP KL K SIA +QMVEI +A+ + A+V+ LDEPTSSL+ +ET Sbjct: 117 AKRFVRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRET 176 Query: 178 EKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGT-DSIENLTKEKIVEM 236 E LF++V+ L+ A+I+ISHR++EI+E+CD ++ RDG I + ++E +T++ IV Sbjct: 177 EVLFKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSE 236 Query: 237 MVGRKLEKFYIKEAHEPGEVVLEVKNLSGERF-ENVSFSLRRGEILGFAGLVGAGRTELM 295 MVGR++ Y A GEV K + G + SF +RRGEI+GF GLVGAGR+ELM Sbjct: 237 MVGREISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELM 296 Query: 296 ETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPS 355 ++G K+GGE+ ++GK +++ +AI GI L PEDRK+ G++ + ++ N+++ Sbjct: 297 HLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISC 356 Query: 356 LDR-IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKP- 413 ++ G F+ K+E E AD IK I+ +K+ +LSGGNQQK +L++WLA +P Sbjct: 357 RRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLA-EPD 415 Query: 414 -KILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKL 472 K++ILDEPTRGIDVGAK EIY ++ QLA+ G ++MISSELPEVL +SDRI VM G++ Sbjct: 416 LKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRI 475 Query: 473 AGIIDAKEASQEKVMKLA 490 +G + K+A+++ V+ LA Sbjct: 476 SGELTRKDATEQSVLSLA 493 Lambda K H 0.318 0.138 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: 675 Number of extensions: 37 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: 494 Length of database: 512 Length adjustment: 34 Effective length of query: 460 Effective length of database: 478 Effective search space: 219880 Effective search space used: 219880 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: 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