Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 290 bits (741), Expect = 1e-82 Identities = 183/485 (37%), Positives = 264/485 (54%), Gaps = 19/485 (3%) Query: 4 TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63 TP++++ GI KSFG A D+ L I PG I AL+GENGAGKSTLM +LSG A D G I Sbjct: 32 TPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGII 91 Query: 64 LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123 +DG V R P + AGI ++YQ + +++VA NV +G G SR Sbjct: 92 HVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQS-----GAWLSPVHMSR 146 Query: 124 TDAVLRQLGAGFGAS-DLAGR---LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERET 179 V+ +L A +G D A R LS+ E+Q+VEI + L SR++I+DEPTA L+ ET Sbjct: 147 ---VVAELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGET 203 Query: 180 EQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSE-RIVQM 238 EQLF + R+ + G AI++ISH+M EV ALAD + +LR G V E E+ E + Sbjct: 204 EQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANR 263 Query: 239 MVGRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGR 298 MVGR + + + P D V+ V LAG ++ SF+VR GEV AG+ G G+ Sbjct: 264 MVGREVILEVAAEPLEPGDR-----VLHVDGLAGDGLKGLSFEVRKGEVFAIAGVAGNGQ 318 Query: 299 TELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANA 358 EL + G + G++ L G P +A + G+AY+PEDR+G L + + N Sbjct: 319 RELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNF 378 Query: 359 TMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEI 418 + TR + +S AR + NV+ E P LSGGN QK+++ R Sbjct: 379 LLTARGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYR 438 Query: 419 APKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGM 478 P +++ + PT+G+DI A E++ + + S V+++S +L EV+ + DRV VM G Sbjct: 439 KPSLIVAENPTQGLDIAATEEVWARLLEVRSH-AGVLLVSGDLNEVLALADRVAVMYRGC 497 Query: 479 ITGEL 483 G L Sbjct: 498 FIGLL 502 Score = 79.3 bits (194), Expect = 3e-19 Identities = 62/236 (26%), Positives = 107/236 (45%), Gaps = 20/236 (8%) Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338 + D+ G + G GAG++ L +L G + G I ++G V P+ A++AGI Sbjct: 54 TLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAGIGM 113 Query: 339 VPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETP 398 V + L M VA N + + + + V R + + P Sbjct: 114 VYQHFM---LVDSMTVAENVLLGQSG-----AWLSPVHMSRVVAELAARYGLDI-DPAAR 164 Query: 399 VGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVIS 458 V LS G +Q+V + + L +VLILDEPT + ++++ +HR+A G A+V IS Sbjct: 165 VCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAENGKAIVFIS 224 Query: 459 SELPEVIGICDRVLVMREGMIT-----------GELAGAAITQENIMRLATDTNVP 503 ++ EV+ + D + ++R G + ELA + +E I+ +A + P Sbjct: 225 HKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREVILEVAAEPLEP 280 Score = 73.2 bits (178), Expect = 2e-17 Identities = 59/228 (25%), Positives = 108/228 (47%), Gaps = 7/228 (3%) Query: 22 LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAA 81 L + +R GE+ A+ G G G+ L++ ++G+ P +GE+ L G P A R Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG 354 Query: 82 GINLIYQE---LAVAPNISVAANVFMGSE-LRTRLGLIDHAAMRSRTDAVLRQLGAGFGA 137 G+ I ++ LA ++ + N + + TR +D + + +L + G Sbjct: 355 GLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAARDILAEYNVQPGR 414 Query: 138 SDLAGR-LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAI 196 ++ R LS Q++ + R + +++ + PT L TE+++ + +R + Sbjct: 415 AEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA-GV 473 Query: 197 IYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDS-ERIVQMMVGRS 243 + +S + EV ALADRV V+ G F+G L R + + + I MM G S Sbjct: 474 LLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMMAGVS 521 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: 697 Number of extensions: 48 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 521 Length of database: 524 Length adjustment: 35 Effective length of query: 486 Effective length of database: 489 Effective search space: 237654 Effective search space used: 237654 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