Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= TCDB::Q9X051 (523 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 344 bits (882), Expect = 5e-99 Identities = 192/493 (38%), Positives = 298/493 (60%), Gaps = 10/493 (2%) Query: 13 LEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFLE 72 ++ R ITK + GV A+++V + GE L GENG+GKSTL+KI++GV P G + + Sbjct: 10 IDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIA 69 Query: 73 GKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQASK 132 G+E NPR + G+ +I Q+ L PNLS AENI + + + +++ + + A Sbjct: 70 GQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARA 129 Query: 133 LFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNII 192 ++GV ID +VE L +Q+Q+VAI +AL+ A++IIMDEPT+A+ ++E +L II Sbjct: 130 ALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGII 189 Query: 193 RSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRSIDQ 252 R LK EG +VI++SH+L E+ E++++VVV+R+G+KV EGP EFD L M GR + + Sbjct: 190 RMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDVPE 249 Query: 253 FFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTELLEA 312 + A + +V+G+ K D+SF +R GEVLGI GL+G GRT + +A Sbjct: 250 VPPSDVAAGAQTLMQVQGL------GKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKA 303 Query: 313 IFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITLPSV 372 +FG G + + G + + P+ A IG VPEDR T GL L S+L N+ + + Sbjct: 304 LFGL-VTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRL 362 Query: 373 VMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIKP 432 G +D + ++ +L +K P V++LSGGNQQ+V LA+WL+ P Sbjct: 363 DAH---TSGGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAP 419 Query: 433 KVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVMSEGRKT 492 +VL+L+ P+ G+DV +K++I+ +I E+A G+GV+++S +LPE+LA R+LVM EGR Sbjct: 420 RVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRII 479 Query: 493 AEFLREEVTEEDL 505 +TE+DL Sbjct: 480 DALEGTALTEDDL 492 Lambda K H 0.317 0.137 0.372 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: 534 Number of extensions: 30 Number of successful extensions: 8 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: 523 Length of database: 498 Length adjustment: 34 Effective length of query: 489 Effective length of database: 464 Effective search space: 226896 Effective search space used: 226896 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 (21.6 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