Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate RR42_RS12250 RR42_RS12250 sulfate ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__Cup4G11:RR42_RS12250 Length = 374 Score = 237 bits (604), Expect = 4e-67 Identities = 119/242 (49%), Positives = 165/242 (68%), Gaps = 4/242 (1%) Query: 18 VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77 +Q+ ++K F + + L + G+ LLGPSGCGKTT+LR+IAGLE D+G+I+L+ Sbjct: 3 IQVKNVQKHFGNFVALDDVTLDFDEGQLTALLGPSGCGKTTLLRIIAGLERADAGQILLE 62 Query: 78 NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRM----QKTPAAEITPRVMEALR 133 D +H R V VFQ YALF HMTVFENVAFGLR+ ++ A+I +V L Sbjct: 63 GRDASHQHVRQRQVGFVFQHYALFKHMTVFENVAFGLRVKPRAERPGEAQIRDKVRALLE 122 Query: 134 MVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKAL 193 +VQL+ A R P QLSGGQ+QR+A+ARA+ +PR+LLLDE ALD K+RK+++ L+ L Sbjct: 123 LVQLDWLADRYPPQLSGGQRQRIALARALAVEPRVLLLDEPFGALDAKVRKELRRWLRRL 182 Query: 194 QRKLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINM 253 +L +T VFVTHDQEEAL ++D++V+M G +EQ GTP +Y P FV GF+G +N+ Sbjct: 183 HDELHVTSVFVTHDQEEALEVADQVVLMNRGHVEQAGTPEAVYNHPATPFVFGFLGNVNL 242 Query: 254 FN 255 F+ Sbjct: 243 FH 244 Lambda K H 0.319 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: 365 Number of extensions: 17 Number of successful extensions: 2 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: 378 Length of database: 374 Length adjustment: 30 Effective length of query: 348 Effective length of database: 344 Effective search space: 119712 Effective search space used: 119712 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 (21.7 bits) S2: 50 (23.9 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