Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__Marino:GFF1380 Length = 362 Score = 241 bits (616), Expect = 2e-68 Identities = 136/302 (45%), Positives = 189/302 (62%), Gaps = 24/302 (7%) Query: 18 VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77 +++ GI K FD + + ++LTI +G+ LLGPSG GKTT+LR+IAGLET + GRI Sbjct: 3 IEIQGINKFFDKFQALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIRFS 62 Query: 78 NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGL----RMQKTPAAEITPRVMEALR 133 +D+T + +R V VFQ YALF HMTV ENVAFGL R ++ EI RV + L Sbjct: 63 GKDVTDLHVRDRRVGFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRVKDLLE 122 Query: 134 MVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKAL 193 MVQLE A R P QLSGGQ+QR+A+ARA+ +P +LLLDE ALD K+RK ++ L++L Sbjct: 123 MVQLEHLADRYPAQLSGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRRWLRSL 182 Query: 194 QRKLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINM 253 +L T VFVTHDQEEAL +SD++VVM +GRIEQ TP E+Y P + FV F+G++N+ Sbjct: 183 HDELHFTSVFVTHDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLGQVNV 242 Query: 254 FNATVIERLDEQ-----RVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRV-EEINDD 307 + + + + Q R+ E + +Y LRP ++R+ + +DD Sbjct: 243 LSGKIRDGVMRQGDAWIRLPEGCENDDAQLY--------------LRPHEVRLTQSASDD 288 Query: 308 NH 309 H Sbjct: 289 AH 290 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: 359 Number of extensions: 12 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: 362 Length adjustment: 30 Effective length of query: 348 Effective length of database: 332 Effective search space: 115536 Effective search space used: 115536 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: 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