Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS16965 RR42_RS16965 ABC transporter
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__Cup4G11:RR42_RS16965 Length = 258 Score = 192 bits (487), Expect = 9e-54 Identities = 116/266 (43%), Positives = 158/266 (59%), Gaps = 18/266 (6%) Query: 10 SDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMG 69 +++ LL V+ ++ +FGGL A++D + K G+I LIGPNGAGKTT FN ITG Y P G Sbjct: 3 NENLLLSVQGVNKRFGGLQALSDVGLQIKPGEIYGLIGPNGAGKTTFFNVITGLYTPDSG 62 Query: 70 MITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASG 129 GK Y + + +A +ARTFQNIRLF +T LEN++V +H + Sbjct: 63 EFVL---GGKAYQPTAVHE---VAKAGIARTFQNIRLFGEMTALENVMVGRHVR------ 110 Query: 130 YTILGLIGV----GPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARA 185 T GL G +RE + A LE + A + +L YG QRRLEIARA Sbjct: 111 -TKAGLFGAVFRPPSVRREEHSVEDWAHDLLEYVGIGKYAHFTSRNLSYGHQRRLEIARA 169 Query: 186 MCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVL 245 + T P+LL LDEPAAG+N E L LL IR++ G +ILLIEHD+ +VM + + + VL Sbjct: 170 LATEPKLLALDEPAAGMNATEKVELRGLLDKIRSD-GKTILLIEHDVKLVMGLCNRLTVL 228 Query: 246 EYGQKISDGTPDHVKNDPRVIAAYLG 271 +YG+ I+ G P V+++P VI AYLG Sbjct: 229 DYGKVIAQGLPHEVQSNPAVIEAYLG 254 Lambda K H 0.318 0.136 0.386 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: 207 Number of extensions: 12 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: 292 Length of database: 258 Length adjustment: 25 Effective length of query: 267 Effective length of database: 233 Effective search space: 62211 Effective search space used: 62211 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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