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:D8J111 (520 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 276 bits (706), Expect = 1e-78 Identities = 172/504 (34%), Positives = 278/504 (55%), Gaps = 18/504 (3%) Query: 6 ETSTTGVAASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLM 65 +T TG A + PV+ L + K F V A + ++ G + AL+GENGAGKSTLM Sbjct: 19 QTGRTGRALRHDVT-PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLM 77 Query: 66 KILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPR 125 ILSG +D+G I +DG+ V P+ A GIG+++Q L++ ++ A+N+ +G+ Sbjct: 78 SILSGRLAQDTGIIHVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQS-- 135 Query: 126 KAMGLFIDEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMD 185 G ++ ++R A + AR LD+DP+ V +L++ +Q VEI K L DSRVLI+D Sbjct: 136 ---GAWLSPVHMSRVVAELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILD 192 Query: 186 EPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQ 245 EPTA L E +LF + + G IV+ISHKM E+ +AD ++++R G+ + Sbjct: 193 EPTAVLTPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHES 252 Query: 246 ETSMDT-IISMMVGRALDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGF 304 E + + + MVGR + E P D VL V GL G ++ +SF +RKGE+ Sbjct: 253 EVPGEAELANRMVGREVILEVAAEP-LEPGDRVLHVDGL-AGDGLKGLSFEVRKGEVFAI 310 Query: 305 AGLMGAGRTEVARAIFGADPLEAGEIIIHG---GKAVIKSPADAVAHGIGYLSEDRKHFG 361 AG+ G G+ E+ + G GE+ + G + K+P G+ Y+ EDR+ Sbjct: 311 AGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG---GLAYIPEDRQGLA 367 Query: 362 LAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQ 421 + +D+ N L++ G FTR F+D+++ AA+ + + ++ E AR LSGGN Sbjct: 368 TCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNL 427 Query: 422 QKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIY-KLLDALAEQGKAIVMISSELPEVLR 480 QK+V+ + R ++ + PT+G+D+ A E++ +LL+ + G ++++S +L EVL Sbjct: 428 QKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHAG--VLLVSGDLNEVLA 485 Query: 481 MSHRVLVMCEGRITGELARADATQ 504 ++ RV VM G G L R+D + Sbjct: 486 LADRVAVMYRGCFIGLLDRSDTNK 509 Score = 96.3 bits (238), Expect = 2e-24 Identities = 71/241 (29%), Positives = 115/241 (47%), Gaps = 19/241 (7%) Query: 273 RNDV--VLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLE 326 R+DV V+ + G+ + RA D++ + G I G GAG++ + + G + Sbjct: 28 RHDVTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQD 87 Query: 327 AGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFM 386 G I + G +SP DA+ GIG + + HF L M V N+ L G + M Sbjct: 88 TGIIHVDGEAVRFRSPKDALKAGIGMVYQ---HFMLVDSMTVAENVLLGQSGAWLSPVHM 144 Query: 387 DQRAIREAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTR 444 R + E A Y ++ AR+ LS G +Q++ I K L RD +L DEPT Sbjct: 145 S-RVVAELAARYGLD-------IDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTA 196 Query: 445 GIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQ 504 + G ++++ L +AE GKAIV IS ++ EVL ++ + ++ G + E ++ Sbjct: 197 VLTPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPG 256 Query: 505 E 505 E Sbjct: 257 E 257 Lambda K H 0.320 0.135 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: 647 Number of extensions: 35 Number of successful extensions: 9 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: 520 Length of database: 524 Length adjustment: 35 Effective length of query: 485 Effective length of database: 489 Effective search space: 237165 Effective search space used: 237165 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