Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__azobra:AZOBR_RS30410 Length = 371 Score = 277 bits (708), Expect = 4e-79 Identities = 158/326 (48%), Positives = 207/326 (63%), Gaps = 6/326 (1%) Query: 18 VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77 V++ G+ + V+ + L I GEF LGPSGCGKTT+LRLIAG T G + + Sbjct: 19 VRIDGVDLSYGSHRVLKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTIG 78 Query: 78 NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQL 137 DI+ +PA R V VFQSYAL+PHMTV NVAFGL ++ P AEI RV AL +V L Sbjct: 79 GRDISGLPAHKRDVGMVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALDLVGL 138 Query: 138 ETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKL 197 + A R+P QLSGGQQQRVA+AR +V +P++LLLDE LS LD KLR QM+ EL +LQRKL Sbjct: 139 KHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRKL 198 Query: 198 GITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNAT 257 G+T +FVTHDQEEA T+ DRI VM DG ++Q GTP+E+Y+ P NLFVAGF+G N+ Sbjct: 199 GLTTIFVTHDQEEANTICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGTANVLEGQ 258 Query: 258 VIERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEINDDNHA--EGLIG 315 V +D A V G I + VEPG ++ RP++L + + A L+G Sbjct: 259 V-RAVDGG--TAFVMGGGVPIPLPHGVEPGAAGKLMFRPQNLFIRQDGGPPRAGHVRLMG 315 Query: 316 YVRERNYKGMTLESVVELENGKMVMV 341 VR R + G ++ V++ G+ V V Sbjct: 316 VVRHREFLGASIRYAVDI-GGQQVQV 340 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: 334 Number of extensions: 15 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: 371 Length adjustment: 30 Effective length of query: 348 Effective length of database: 341 Effective search space: 118668 Effective search space used: 118668 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