Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein
Query= uniprot:D8IUD1 (522 letters) >FitnessBrowser__Cup4G11:RR42_RS30800 Length = 530 Score = 273 bits (697), Expect = 1e-77 Identities = 190/524 (36%), Positives = 275/524 (52%), Gaps = 26/524 (4%) Query: 11 SPLLTLSGIGKRYAAPVL-DGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGM 69 +P+L L+GI KR+ V D I L+L+ G+VLAL GENGAGKSTL I+ G A AG + Sbjct: 3 TPILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTV 62 Query: 70 MLDGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPRRFGWIDRKKLAEAA 129 +DGQP P A GI MV Q L LS+ +N+ L P +D Sbjct: 63 EVDGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAARGKV 122 Query: 130 RAQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLF 189 A E GL + P VG+L +G +Q VEI + L R LILDEPTA+LT E E LF Sbjct: 123 LALAERFGLA-VRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLF 181 Query: 190 SRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMAGEL 249 S + +L AEG+++I+ISH+L+E+ R++DRI VLR GKLV + + +L +LM G + Sbjct: 182 STLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRV 241 Query: 250 TKVD--------LDAEHRRIGAPVLRIRGLGR-----APVVHPASLALHAGEVLGIAGLI 296 + D + PVL + +G ++ SL + AGE++GIAG+ Sbjct: 242 VAMPERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVS 301 Query: 297 GSGRTELLRLIFGADRAEQGEIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQ 356 G+G+ L L G A +G I + A+ P+ + AG+A V EDR G++ Sbjct: 302 GNGQAALAELASGMLEASEGRITLAGKPMSAK---PRAWIGAGVARVPEDRHAIGVVGDL 358 Query: 357 AISVNTSLANLGS--VSRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKV 414 A+ N L SR G++ AA A+D V + +R+ + A +SGGN QK+ Sbjct: 359 AVWENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKL 418 Query: 415 VIARWL----YRDCP-IMLFDEPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELM 469 ++ R L P +++ +PT G+DIGA + + + A +G +L++S DL EL Sbjct: 419 ILGRALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLDELH 478 Query: 470 QICDRIAVMSAGRIADTFSRDDWSQERILAAAFSGYVGRQEAAA 513 + DRIAVM AG + + W+ L A +G G Q A A Sbjct: 479 ALADRIAVMHAGHLTEARPTAAWTLGE-LGLAMAGSGGGQHAQA 521 Lambda K H 0.320 0.137 0.390 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: 780 Number of extensions: 36 Number of successful extensions: 10 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: 522 Length of database: 530 Length adjustment: 35 Effective length of query: 487 Effective length of database: 495 Effective search space: 241065 Effective search space used: 241065 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