Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 336 bits (861), Expect = 1e-96 Identities = 182/483 (37%), Positives = 288/483 (59%), Gaps = 13/483 (2%) Query: 18 PAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEI 77 P +L+ RG+ + F ALD V +AL G V AL+G+NGAGKSTL+K+LTG+ RP+ G + Sbjct: 10 PVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSV 69 Query: 78 LVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTR-FRTIDWQTMNS 136 +DGR ++ A G+ ++QE L L+VAEN++ G PR R R IDW+ + Sbjct: 70 ELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRD 129 Query: 137 RSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDL 196 +++LL L +D L +A R +VAIARAL + AR++I+DEPT++L E+ +L Sbjct: 130 GARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVREL 189 Query: 197 FRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVG 256 FR++ L+E+G AILF++H D++Y ++D V R V+ P +V MVG Sbjct: 190 FRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVA-DLPPAALVNAMVG 248 Query: 257 RDVENVF-------PKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGR 309 RD+ V P D P ++ + R + + +R+GE+LG+ GL+G+GR Sbjct: 249 RDLPTVAGADAERAPPPDAP---PAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGR 305 Query: 310 SELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNM 369 +EL++ LFG+ + G++ + G+ + + P DA+ G+ PEER G+ + + +N+ Sbjct: 306 TELARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENI 365 Query: 370 TLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLAT 429 L AR RG RA + LAR+ + L ++AA + PVG LSGGNQQKV++ +WL T Sbjct: 366 VLALQARQGWRGMSRARQD-ELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVT 424 Query: 430 APKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGL 489 P+++ILDEPT+GID+ +K + ++ A G++++ +S+E E+ DR+ VM+E Sbjct: 425 EPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERR 484 Query: 490 SAG 492 AG Sbjct: 485 KAG 487 Score = 99.4 bits (246), Expect = 3e-25 Identities = 67/222 (30%), Positives = 111/222 (50%), Gaps = 4/222 (1%) Query: 289 ISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIV 348 + LR GE+ + G GAG+S L + L G+ +P G + L+G+ I +P +A R GI Sbjct: 31 VDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVELDGRVIAPSTPMEAQRDGIG 90 Query: 349 YVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSV 408 V +E L + + +N+ R R + AR +L L + Sbjct: 91 TVYQEVN---LCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGARSLLRQLHLELD-VDA 146 Query: 409 PVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMV 468 P+G+ +Q V I + L + +V+ILDEPT +D G + I++L G++I+ V Sbjct: 147 PLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELFRVIAQLRERGMAILFV 206 Query: 469 SSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510 + L ++ +SDR+ V+++G G + A+L P ALV A G Sbjct: 207 THFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVG 248 Lambda K H 0.320 0.137 0.382 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: 571 Number of extensions: 32 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: 512 Length of database: 505 Length adjustment: 34 Effective length of query: 478 Effective length of database: 471 Effective search space: 225138 Effective search space used: 225138 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