Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 393 bits (1009), Expect = e-114 Identities = 221/498 (44%), Positives = 310/498 (62%), Gaps = 8/498 (1%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 +LQ RG+ K FGATLAL + L +R GE+HALMG+NGAGKSTL+K+L+GV PD+G + L Sbjct: 12 VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVEL 71 Query: 66 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGS-ELRTRLGLIDHAAMRSRT 124 DGR +A P ++ GI +YQE+ + PN+SVA N++ G R RL +ID +R Sbjct: 72 DGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGA 131 Query: 125 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184 ++LRQL G +A +Q V IARAL +R++I+DEPT++L E E +LF Sbjct: 132 RSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELFR 191 Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244 V+ +LR+ G+AI++++H + +VYA++DR+TVLRDG VGE ++ +V MVGR L Sbjct: 192 VIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVGRDL 251 Query: 245 SEFY--QHQRIAPADAAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGAGRTEL 301 +R P DA P + + L GK+ P VR GE+LG GL+G+GRTEL Sbjct: 252 PTVAGADAERAPPPDA---PPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTEL 308 Query: 302 ARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMN 361 ARLLFG D G++ + G V + P A+ G+A PE+RK G+ +++V N + Sbjct: 309 ARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVLA 368 Query: 362 VASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPK 421 + +R G+ R+R +AR +Q L +K A ETPVG LSGGNQQKV+LARWL P+ Sbjct: 369 LQARQGWRGMSRARQ-DELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEPR 427 Query: 422 VLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITG 481 +LILDEPTRG+D+ AK E+ V R A G+AV+ IS+E E+ CDR+ VMRE G Sbjct: 428 LLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRKAG 487 Query: 482 ELAGAAITQENIMRLATD 499 EL G + + +A D Sbjct: 488 ELPGGSTEARVLAMIAGD 505 Score = 114 bits (284), Expect = 1e-29 Identities = 81/272 (29%), Positives = 139/272 (51%), Gaps = 10/272 (3%) Query: 253 IAPADAAQLPTVMQVRALA---GGKIRPASFDV--RAGEVLGFAGLVGAGRTELARLLFG 307 + P A P V+Q R L G + D+ RAGEV G GAG++ L +LL G Sbjct: 1 MTPVSPAARPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTG 60 Query: 308 ADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHT 367 + G + L+GR + P A R GI V ++ L ++VA N R Sbjct: 61 VERPDRGSVELDGRVIAPSTPMEAQRDGIGTVYQE---VNLCPNLSVAENLYAGRYPRRR 117 Query: 368 RLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDE 427 RL ++ R + AR+ +++L++++ + P+G +Q V +AR L ++ +VLILDE Sbjct: 118 RLRMIDWRQVRDGARSLLRQLHLEL-DVDAPLGSYPVAIRQMVAIARALGVSARVLILDE 176 Query: 428 PTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAA 487 PT +D E+++++ +L +G+A++ ++ L +V + DR+ V+R+G GE A A Sbjct: 177 PTSSLDEGEVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVAD 236 Query: 488 ITQENIMRLATDTNVPRTAPA-SHSSPTPLAP 518 + ++ ++P A A + +P P AP Sbjct: 237 LPPAALVNAMVGRDLPTVAGADAERAPPPDAP 268 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: 764 Number of extensions: 40 Number of successful extensions: 8 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: 505 Length adjustment: 35 Effective length of query: 486 Effective length of database: 470 Effective search space: 228420 Effective search space used: 228420 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 Apr 09 2024. 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