Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate HSERO_RS11485 HSERO_RS11485 ribose ABC transporter ATPase
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__HerbieS:HSERO_RS11485 Length = 522 Score = 396 bits (1018), Expect = e-115 Identities = 227/504 (45%), Positives = 317/504 (62%), Gaps = 15/504 (2%) Query: 15 SSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQR 74 S S P++ L + KR+ + LD +L G+V AL GENGAGKSTL KI+ G+ Sbjct: 6 SLSQGSPLLTLSGIGKRYAAPV-LDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDA 64 Query: 75 DSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDE 134 +G ++LDG+P QA+ LGI ++ QELNL+ LS A+N+F+ + PR+ +ID Sbjct: 65 SAGGMMLDGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPRRFG--WIDR 122 Query: 135 DELNRQAAAIFARMRL-DMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNN 193 +L A A + L ++DP TPVG+L + QQMVEIA+ L R LI+DEPTA L N Sbjct: 123 KKLAEAARAQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTN 182 Query: 194 AEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTII 253 E+ LF I L+A+GV I+YISH+++EL++IADR+ V+RDGK + + S + ++ Sbjct: 183 REVELLFSRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLV 242 Query: 254 SMMVGRA----LDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMG 309 +M G LD E R VL +RGL R + S L GE+LG AGL+G Sbjct: 243 QLMAGELTKVDLDAEHR-----RIGAPVLRIRGLGRAPVVHPASLALHAGEVLGIAGLIG 297 Query: 310 AGRTEVARAIFGADPLEAGEIIIHGGK--AVIKSPADAVAHGIGYLSEDRKHFGLAVGMD 367 +GRTE+ R IFGAD E GEI I + A I+SP DAV GI ++EDRK GL + Sbjct: 298 SGRTELLRLIFGADRAEQGEIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQA 357 Query: 368 VQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIA 427 + N +L+++G +R G +D A AQ YV++L I++ SV Q A LSGGNQQK+VIA Sbjct: 358 ISVNTSLANLGSVSRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIA 417 Query: 428 KWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLV 487 +WL RDC I+ FDEPTRGID+GAKS+IY+L LA QGK ++++SS+L E++++ R+ V Sbjct: 418 RWLYRDCPIMLFDEPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAV 477 Query: 488 MCEGRITGELARADATQEKIMQLA 511 M GRI +R D +QE+I+ A Sbjct: 478 MSAGRIADTFSRDDWSQERILAAA 501 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: 636 Number of extensions: 24 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: 520 Length of database: 522 Length adjustment: 35 Effective length of query: 485 Effective length of database: 487 Effective search space: 236195 Effective search space used: 236195 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