Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate BPHYT_RS20685 BPHYT_RS20685 ribose ABC transporter ATPase
Query= uniprot:A0A165ZSX8 (514 letters) >FitnessBrowser__BFirm:BPHYT_RS20685 Length = 537 Score = 365 bits (936), Expect = e-105 Identities = 216/496 (43%), Positives = 302/496 (60%), Gaps = 11/496 (2%) Query: 16 LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75 LR +GIGK++ LA++S H G+V AL GENGAGKSTL KI+GG P++G + + Sbjct: 15 LRVHGIGKTY-AEPVLADVSLDLHAGEVLALTGENGAGKSTLSKIIGGLVTPTTGSMTLA 73 Query: 76 EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPAR--FGLVNRGVLRQQAL 133 D+ A GV ++ QEL+L+P ++VAENLFL LP R FG ++R LR+ A Sbjct: 74 GAAYTPASRKDAEALGVRMVMQELNLLPTLSVAENLFLNRLPQRGIFGWIDRAKLREDAR 133 Query: 134 TLLKGLA-DEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMA 192 + + D IDP VG L +G +Q+VEIA+ L V+ DEPT+ L+ARE+D L Sbjct: 134 HAMAQVGLDAIDPDTLVGTLGIGHQQMVEIARNLIGDCRVLILDEPTAMLTAREVDLLFE 193 Query: 193 IIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRD 252 + RL+ G ++Y+SHR+EE+ RI V +DGR V E M+ LT D+LVT MVGRD Sbjct: 194 QVERLKARGVALVYISHRLEELKRIARRAAVLRDGRLVHVDE-MANLTTDRLVTLMVGRD 252 Query: 253 IQDIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSG 312 I D D R G++ +V G+ + VSF+V GEI G+ GL+GAGRTEL+RL+ G Sbjct: 253 IGDRIDLGERRIGEMTFKVSGMTREPVVRDVSFEVKAGEIFGISGLIGAGRTELMRLIYG 312 Query: 313 LERQREG--SLVLHDKELK---LRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISA 367 +R G S+V L+ + SP DA+ G+ L EDRK EG++ + NI++ Sbjct: 313 ADRADAGTVSIVREGGALEPVTIASPSDAVKHGIALITEDRKGEGLLLTQPIAANISLGH 372 Query: 368 RPSHSTLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMK 427 S S+ G ++ G E A +QI ++++++ Q + LSGGNQQK ++GRWL+ Sbjct: 373 LRSVSSKG-VVDGRREASLARRQIDAMRIRSSGPAQPVSELSGGNQQKVVIGRWLARDCT 431 Query: 428 VLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRG 487 VLL DEPTRGID+GAK +IY ++ LA +G A++VVSSDL E+M I DRI V+ G M G Sbjct: 432 VLLFDEPTRGIDVGAKFDIYALMGALAREGRALVVVSSDLRELMAICDRIAVMSAGRMTG 491 Query: 488 ELSRDQANESNLLQLA 503 R + LL A Sbjct: 492 LFERGNWTQDALLAAA 507 Lambda K H 0.320 0.138 0.391 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: 728 Number of extensions: 52 Number of successful extensions: 10 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: 514 Length of database: 537 Length adjustment: 35 Effective length of query: 479 Effective length of database: 502 Effective search space: 240458 Effective search space used: 240458 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