Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate RR42_RS37305 RR42_RS37305 sulfate ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Cup4G11:RR42_RS37305 Length = 366 Score = 223 bits (568), Expect = 6e-63 Identities = 130/301 (43%), Positives = 180/301 (59%), Gaps = 8/301 (2%) Query: 4 LEIRNIRKRYGEV---ETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 L + + KR+G + L G+ +++ GE L LLG SGCGK+TLL IIAGL G I Sbjct: 13 LAVEQVGKRFGGAGGFQALDGVSLSVAQGELLCLLGPSGCGKTTLLRIIAGLEREDTGRI 72 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 G R + G+ P+ RD ++FQSYAL+PNLSVARN+ +GL+ R + +A + V + L Sbjct: 73 HAGGRELTGLPPQARDYGILFQSYALFPNLSVARNVAYGLQGRGMGRAHREARVAEMLSL 132 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 + + + P QLSGGQ+QRVA+ RAL P + L DEP+S LDA++R +R EL++L Sbjct: 133 VGLAGSERKFPGQLSGGQQQRVALARALAPAPSLLLLDEPMSALDARVREHLRLELRQLQ 192 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 + L T V VTHDQ EAM +A RIAVM GRI Q+ P E+Y+RPA+ +VA F+G N Sbjct: 193 RRLNVTTVMVTHDQDEAMAMADRIAVMEGGRIAQVGTPGEIYERPASAFVAEFIGQ--AN 250 Query: 241 ILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRL-AAGSEAQRLTAS 299 LD ++ G ++ PA + A R + RPEA+RL E RL A Sbjct: 251 WLDGRLSGRDTFSVGELDLAVSPARASEVADGAAR--LCCRPEAIRLHPVEGEPNRLLAR 308 Query: 300 V 300 + Sbjct: 309 I 309 Lambda K H 0.320 0.136 0.385 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: 348 Number of extensions: 17 Number of successful extensions: 1 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: 360 Length of database: 366 Length adjustment: 29 Effective length of query: 331 Effective length of database: 337 Effective search space: 111547 Effective search space used: 111547 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: 49 (23.5 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