Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate BPHYT_RS22015 BPHYT_RS22015 spermidine/putrescine ABC transporter ATPase
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__BFirm:BPHYT_RS22015 Length = 363 Score = 259 bits (663), Expect = 6e-74 Identities = 143/294 (48%), Positives = 187/294 (63%), Gaps = 18/294 (6%) Query: 20 LAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNE 79 L + K F + + ++L++ GEF++LLGPSGCGKTT L++IAG GRI LD Sbjct: 6 LTDVTKSFGDLQAVADVNLSVEKGEFVSLLGPSGCGKTTTLQMIAGFVETTHGRITLDGR 65 Query: 80 DITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLET 139 DITH+ R + VFQSYALFPHM+V +NV FGL M+ AE R+ EAL +V+L+T Sbjct: 66 DITHMKPNKRGLGIVFQSYALFPHMSVADNVGFGLEMRNIDKAERKERIREALSLVRLDT 125 Query: 140 FAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGI 199 A R P +LSGGQ+QRVA+ARA+V P +LLLDE +S LD KLR+ MQ EL+ +QRK+G Sbjct: 126 LAHRFPRELSGGQRQRVALARAIVIAPPVLLLDEPMSNLDAKLREDMQFELRGIQRKIGT 185 Query: 200 TFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNATVI 259 T + VTHDQ EAL++SDR+VVM GRI Q TP E YE P+N FV+ FIG+ NM TV+ Sbjct: 186 TTIMVTHDQSEALSISDRVVVMEAGRITQIDTPYEAYERPENRFVSQFIGKANMLPGTVV 245 Query: 260 ER------------LDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRV 301 R L E A + RE + V G + + +RPE LR+ Sbjct: 246 ARDGDAIRIDLGHDLAETGHTAQLPARERVVGV------GDAVTLCIRPEKLRL 293 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: 303 Number of extensions: 10 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: 378 Length of database: 363 Length adjustment: 30 Effective length of query: 348 Effective length of database: 333 Effective search space: 115884 Effective search space used: 115884 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