Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >MicrobesOnline__882:209027 Length = 368 Score = 402 bits (1033), Expect = e-117 Identities = 209/361 (57%), Positives = 259/361 (71%), Gaps = 1/361 (0%) Query: 17 LVQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIML 76 +++L G+ K F+ + +DL I NGEFLTLLGPSGCGKTT+LRLI+G E D+G I L Sbjct: 7 IIELRGVTKNFEDTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVITL 66 Query: 77 DNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQ 136 + + P E R VNTVFQ+YALFPHM+V ENV FGLRMQ+ P EI RV +ALRMV Sbjct: 67 KGQRMDDAPPEARQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALRMVH 126 Query: 137 LETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRK 196 LE A R+P QLSGGQQQRVAIARAVVN P +LLLDE SALDYKLRKQMQ E+K LQR+ Sbjct: 127 LEAHADRRPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHLQRQ 186 Query: 197 LGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNA 256 LGITFVFVTHDQEEA MSDR+VVM DG+IEQ G+P+EIYEEP NL+VA F+GEIN+ NA Sbjct: 187 LGITFVFVTHDQEEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVGEINILNA 246 Query: 257 TVIERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEINDDNHA-EGLIG 315 + + A +EG I PG K++VLLRPEDLRV + +D A L G Sbjct: 247 VIAANHGDGLYDAVIEGVTFPIRSQRTFAPGDKVNVLLRPEDLRVYTLTEDRPAGPHLTG 306 Query: 316 YVRERNYKGMTLESVVELENGKMVMVSEFFNEDDPDFDHSLDQKMAINWVESWEVVLADE 375 + E YKG T++ +V L +G+ +M +EFFNEDD D +++ + + ++WV+ WEVVL D Sbjct: 307 RIEESVYKGATVDLIVTLSDGRRLMAAEFFNEDDVDINYNPGETVTVSWVDGWEVVLPDG 366 Query: 376 E 376 E Sbjct: 367 E 367 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: 429 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: 368 Length adjustment: 30 Effective length of query: 348 Effective length of database: 338 Effective search space: 117624 Effective search space used: 117624 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