Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate HSERO_RS03005 HSERO_RS03005 ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__HerbieS:HSERO_RS03005 Length = 361 Score = 246 bits (629), Expect = 5e-70 Identities = 142/296 (47%), Positives = 187/296 (63%), Gaps = 20/296 (6%) Query: 18 VQLAGIRKCF-DGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSG-RIM 75 ++L+ K F +G + LDL I+ GE L LLGPSGCGKTT LR+IAGLE D G R++ Sbjct: 10 IRLSQCAKSFANGTRALQPLDLQIHPGETLVLLGPSGCGKTTTLRMIAGLEFPDEGGRVL 69 Query: 76 LDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMV 135 ED+T +P E R V VFQ+YALFP+M+V EN+A+G++++K A E RV L MV Sbjct: 70 FGEEDVTMLPIEKRGVGMVFQNYALFPNMSVGENIAYGMKIRKIAAGERAERVERLLEMV 129 Query: 136 QLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQR 195 L+ + R+ QLSGGQ+QRVA+ARA+ +PR+LLLDE L+ALD KLR+ ++++L L R Sbjct: 130 HLQGLSHRRVDQLSGGQKQRVALARALAMEPRVLLLDEPLTALDAKLREAVRSDLNKLLR 189 Query: 196 KLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFN 255 LGIT ++VTHDQ EA+ + DRIVVM G+I Q GTP+EIY P N FVA FIG +N Sbjct: 190 SLGITAIYVTHDQGEAMALGDRIVVMERGKISQIGTPQEIYYHPANDFVAEFIGAMN--- 246 Query: 256 ATVIERLDEQRVRANVEGRECNIYVNFAVEP-----GQKLHVLLRPEDLRVEEIND 306 RV V G + P GQ L RPED+ V +I + Sbjct: 247 ----------RVDGIVAGDRLQLPTGTLPLPPDAVAGQPAQALFRPEDVEVIDITE 292 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: 294 Number of extensions: 13 Number of successful extensions: 3 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: 361 Length adjustment: 30 Effective length of query: 348 Effective length of database: 331 Effective search space: 115188 Effective search space used: 115188 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