Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate Ac3H11_2431 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2431 Length = 514 Score = 257 bits (657), Expect = 6e-73 Identities = 175/520 (33%), Positives = 270/520 (51%), Gaps = 36/520 (6%) Query: 1 MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60 M +L+L I K F + A +L + G V+AL+GENGAGKST+M +L G Y D G+ Sbjct: 1 MSNVLRLSHITKRFGKLVANDSISLTLARGEVLALLGENGAGKSTLMSILFGHYVADEGS 60 Query: 61 LLWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120 + G+ P+++ AGIG++HQ L LT+ +N+ LG E + W+ Sbjct: 61 IEVFGQPLPPGQPRAALAAGIGMVHQHFTLADNLTVLDNVLLGSEPL-------WQPFSR 113 Query: 121 EAD---KLLA---KLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTD 174 ++ KLLA + L D VG LS+G++Q VEI K L + ++I+DEPT LT Sbjct: 114 RSEARAKLLAVSQQFGLPVSPDAKVGSLSVGERQRVEILKALYRGAHILILDEPTAVLTP 173 Query: 175 TETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLI 234 E+E+LF + ++ +QG I++ISH++ E+ + V V R G+ +AE T+ L Sbjct: 174 QESEALFDTLAQMVAQGLSIIFISHKLGEVLRVSHRVAVLRQGKLVAEAPAQGTTQGQLA 233 Query: 235 EMMVGRKLEDQYPHLDKAPGDIRLKVDNL-CGPG----VNDVSFTLRKGEILGVSGLMGA 289 + MVG +E + G+ + N+ P +NDVS TLR GEI+ ++G+ G Sbjct: 234 QWMVGHAIEAAERRPAQNVGEPICTLSNVSTAPAGRDRLNDVSLTLRAGEIVAIAGVSGN 293 Query: 290 GRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKE 349 G+ L VL G T+G VTL G + R P ++ G+ I EDR G+V + V E Sbjct: 294 GQVALADVLCGVRAATTGQVTLRGAPLQAR-PAWLVSQGVARIPEDRHAVGVVGDLPVWE 352 Query: 350 NMSLTALR--YFS----RAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQK 403 N LR +F+ RA + A Q A F+V+ + LSGGN QK Sbjct: 353 NAVSERLRGPWFAHPWFRAFWVKRRAARQHA-QRVAETFDVRGGGADAPARSLSGGNMQK 411 Query: 404 VAIARGLMTR----------PKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSS 453 + + R LM P++++ +PT G+D+GA + Q + + G +++L+S Sbjct: 412 LILGRALMPPQDAAGNSAPVPQLIVAHQPTWGLDIGAVMFVQQQLINARDSGAAVLLISD 471 Query: 454 EMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVG 493 ++ EVL + DR+ VMH+G LS E T+E + A G Sbjct: 472 DLDEVLALGDRVAVMHDGRLSEALPAEGWTREAIGLAMAG 511 Lambda K H 0.318 0.137 0.380 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: 555 Number of extensions: 23 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 501 Length of database: 514 Length adjustment: 34 Effective length of query: 467 Effective length of database: 480 Effective search space: 224160 Effective search space used: 224160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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