Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 400 bits (1029), Expect = e-116 Identities = 223/494 (45%), Positives = 305/494 (61%), Gaps = 5/494 (1%) Query: 4 TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63 TPL +MRGI K+F AL D+ I PGE+H L+GENGAGKS+LMKVL GV+ D GE Sbjct: 8 TPLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEF 67 Query: 64 LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRL-GLIDHAAMRS 122 DG PVA+ P + GI +I+QE ++ P + +A N+F+G E R R+ G +D A M + Sbjct: 68 YHDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHA 127 Query: 123 RTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQL 182 +L LG RL +A+QQ VEIA+AL +RI+++DEPTAALS+RETE+L Sbjct: 128 EARRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKL 187 Query: 183 FNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242 F V+ RL+ +G+++IYISHRMAEV+AL DR+T+LRDG VG + + + +V MVGR Sbjct: 188 FAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVGR 247 Query: 243 SLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELA 302 + Y +R A L V V A +G I + VRAGE++G AGLVG+GR+E+A Sbjct: 248 KVDMSYSRERSAQPGEVALD-VRNVSADSG--IADINLQVRAGEIVGLAGLVGSGRSEVA 304 Query: 303 RLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNV 362 R +FGADP G+I + G+ + P A G A +PE RK +GL L V N + Sbjct: 305 RAVFGADPIRQGEIYIFGKRL-TGGPDRARELGAALIPESRKSEGLALIRTVRDNLLLAG 363 Query: 363 ASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKV 422 R R+ +A I RL + LSGGNQQK+++ +WL K+ Sbjct: 364 LRRAFPARWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKL 423 Query: 423 LILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGE 482 I DEPTRG+D+ AK+EI+ L+ L QG V++ISSELPE+I +CDR VMR G I GE Sbjct: 424 FIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGE 483 Query: 483 LAGAAITQENIMRL 496 +A A +T+E I++L Sbjct: 484 VAHAEMTEERILQL 497 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: 752 Number of extensions: 45 Number of successful extensions: 8 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: 521 Length of database: 502 Length adjustment: 35 Effective length of query: 486 Effective length of database: 467 Effective search space: 226962 Effective search space used: 226962 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 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