Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 379 bits (972), Expect = e-109 Identities = 206/498 (41%), Positives = 305/498 (61%), Gaps = 9/498 (1%) Query: 4 TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63 T + +R I K + AL + T++PGE L GENG+GKSTL+K++SGV G + Sbjct: 7 TAFIDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTV 66 Query: 64 LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123 + G+ +P S AAG+ +I+Q+ ++ PN+SVA N+ ++L TR L A+R Sbjct: 67 QIAGQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDI 126 Query: 124 TDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 183 A L ++G L +A++Q V I RAL +++++IMDEPT AL+E+E +L Sbjct: 127 ARAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQ 186 Query: 184 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 243 ++R L++EG+A+I++SH++AEV ++++V VLR+G V E E D++ + M GR Sbjct: 187 GIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRD 246 Query: 244 LSEFYQHQRIAPAD-AAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGAGRTEL 301 + E + P+D AA T+MQV+ L G SFD+R GEVLG GL+G GRT + Sbjct: 247 VPE------VPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSV 300 Query: 302 ARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMN 361 A+ LFG G IL++G PV + P+AA A I YVPEDR +GLFL ++ N + Sbjct: 301 AKALFGLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVG 360 Query: 362 VASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPK 421 HT G + L A ++RL VK E PV LSGGNQQ+V LARWL AP+ Sbjct: 361 RLDAHTSGGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPR 420 Query: 422 VLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITG 481 VLIL+ P+ GVD+ +K++I+ ++ LA +G+ V+VIS +LPE++ C RVLVMREG I Sbjct: 421 VLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIID 480 Query: 482 ELAGAAITQENIM-RLAT 498 L G A+T++++ RLA+ Sbjct: 481 ALEGTALTEDDLAHRLAS 498 Score = 95.5 bits (236), Expect = 4e-24 Identities = 62/229 (27%), Positives = 116/229 (50%), Gaps = 5/229 (2%) Query: 280 FDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYV 339 F V+ GE + AG G+G++ L +++ G +P + G + + G+ PR + AG+ + Sbjct: 30 FTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAGQEHVTLNPRISAAAGVMVI 89 Query: 340 PEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPV 399 +D LF ++VA N TR L + R++ +ARAA+ R+ V++ + V Sbjct: 90 FQDFS---LFPNLSVAENIAFTT-QLSTRQRLFKFRAVRDIARAALDRIGVQI-DLDARV 144 Query: 400 GKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISS 459 L +Q V + R L +++I+DEPT + + ++ L +GVAV+ +S Sbjct: 145 ETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGIIRMLKEEGVAVIFVSH 204 Query: 460 ELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPA 508 +L EV+ + ++V+V+R G E + +++ T +VP P+ Sbjct: 205 KLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDVPEVPPS 253 Lambda K H 0.320 0.135 0.378 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: 603 Number of extensions: 25 Number of successful extensions: 6 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: 521 Length of database: 498 Length adjustment: 34 Effective length of query: 487 Effective length of database: 464 Effective search space: 225968 Effective search space used: 225968 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