Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate RR42_RS04800 RR42_RS04800 ABC transporter
Query= uniprot:D8IUD1 (522 letters) >FitnessBrowser__Cup4G11:RR42_RS04800 Length = 529 Score = 257 bits (657), Expect = 6e-73 Identities = 186/527 (35%), Positives = 285/527 (54%), Gaps = 26/527 (4%) Query: 11 SPLLTLSGIGKRYAAPVL-DGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGM 69 +P L L+ I KRY D + L + PG++ A+ GENGAGKSTL KII G V AG M Sbjct: 6 TPRLALAHISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGDM 65 Query: 70 MLDGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPRR--------FGWID 121 +G A + A LGI MV Q +L TL++AEN+ L LPR + Sbjct: 66 HFNGARAAIHNPHDARNLGIAMVFQHFSLFDTLTVAENIALG-LPRGSKTAAGSPHAGTN 124 Query: 122 RKKLAEAARAQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLT 181 K+LAE R GL L+P V L +G +Q VEI R L+ + LILDEPT++LT Sbjct: 125 MKQLAEQIRETALRYGL-PLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLT 183 Query: 182 NREVELLFSRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQL 241 + V+ LF + +L AEG +I+YISH+L+E++ + V+R G++ D + S L Sbjct: 184 PQAVQTLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASL 243 Query: 242 VQLMAG----ELTKVDLDAEHRRIGAPVLRI-RGLGRAPVVHPASLALHAGEVLGIAGLI 296 +LM G +V + R+ L + R A + SL L AGE++GIAG+ Sbjct: 244 SRLMIGGEPPREARVQTEPGVCRLAVRELSLPRSHAFATELAGISLDLRAGEIVGIAGVS 303 Query: 297 GSGRTELLRLIFGAD-RAEQGEIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLP 355 G+G+ ELL + G D RA + I + + +P + +AG+A V E+R G+G + Sbjct: 304 GNGQQELLAALSGEDVRAARDAITLDN--KPVGKLDARQRRRAGLAFVPEERLGRGAVPG 361 Query: 356 QAISVNTSLANLGS--VSRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQK 413 +++ N L++ + V RG M+ A + +AQ + +LR+++ A LSGGN QK Sbjct: 362 MSLAANILLSHQSAPYVQRG-MISPKAAAGLAQAVIARLRVKASGPHALAKSLSGGNLQK 420 Query: 414 VVIARWLYRDCPIMLFDEPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICD 473 ++ R + +++ +PT G+D+GA + I+ L A G LLVVS +L EL ICD Sbjct: 421 FIVGREIESGPKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVSEELDELFAICD 480 Query: 474 RIAVMSAGRIADTFSRDDWSQERI---LAAAFSGYV-GRQEAAAAAH 516 R+ V++ GR++ + D ++E++ ++ + G GR+E A H Sbjct: 481 RLHVIAKGRLSPSIPTRDATREQVGLWMSGLWEGGPGGRREQEEAVH 527 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: 649 Number of extensions: 38 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: 529 Length adjustment: 35 Effective length of query: 487 Effective length of database: 494 Effective search space: 240578 Effective search space used: 240578 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