Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate RR42_RS01640 RR42_RS01640 ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__Cup4G11:RR42_RS01640 Length = 358 Score = 151 bits (381), Expect = 3e-41 Identities = 113/340 (33%), Positives = 172/340 (50%), Gaps = 34/340 (10%) Query: 9 IIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGA 68 ++ AVA + +PL+ + + + I L++ L ALGLNI+ GYAG L LG AF AVGA Sbjct: 31 VLMAVAFVAIPLLGSEYWFSAILIP--FLIFALAALGLNILTGYAGQLSLGTAAFMAVGA 88 Query: 69 YLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYL 128 Y A NF + GL L ++ A L AA G G P+L+++G YL Sbjct: 89 YA---------AYNFQ----LRIEGLPVLLTFIL--AGLSAAMVGVAFGLPSLRIKGFYL 133 Query: 129 AIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTL 188 A+ TL + L N ++ G+ ++L +FG I++ Sbjct: 134 AVATLAAQFFVVWALTKFPWFSNNSSS-------------GVITAQQLNLFGIAIDTPVK 180 Query: 189 YYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFG 248 Y L+LV V I+ L S GRAWM++R+ ++AA+ +GI KLLAF + + + Sbjct: 181 KYLFVLMLVTVLAIVAKNLVRSSTGRAWMSVRDMDVAAEVIGIPLMRTKLLAFAVSSFYC 240 Query: 249 GVSGAMFG-AFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYV 307 GV+GA++ + G V P+ FSL S ++ M+++GG+G I G LGA + LP L Sbjct: 241 GVAGALYAFCYLGSVEPDGFSLDLSFRVLFMIIIGGVGSILGSFLGAAFILLLPIFLDIA 300 Query: 308 AGPLQAMTDGRLDSAILR--QLLIALAMIIIML-LRPRGL 344 PL A+ +A + QL++ +II L + P GL Sbjct: 301 LPPLAALLHLPFTNAAVSHIQLMVFGGLIIFFLVVEPHGL 340 Lambda K H 0.328 0.144 0.430 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: 321 Number of extensions: 13 Number of successful extensions: 4 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: 358 Length of database: 358 Length adjustment: 29 Effective length of query: 329 Effective length of database: 329 Effective search space: 108241 Effective search space used: 108241 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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