Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__Miya:8500849 Length = 366 Score = 237 bits (605), Expect = 3e-67 Identities = 143/326 (43%), Positives = 195/326 (59%), Gaps = 22/326 (6%) Query: 18 VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77 + LAGI K + V+ L LT+N+GE TLLGPSGCGKT +LRLIAG ET D+G I + Sbjct: 4 ITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTISIG 63 Query: 78 NEDITH------VPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEA 131 E ++ VP + R + VFQ YA++PHM+V +N+ + L++ PAAE T +V+E Sbjct: 64 GEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQVLET 123 Query: 132 LRMVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELK 191 + MV L R P QLSGGQQQRVA+ARA+V +P L+LLDE L LD LR++M+ E+K Sbjct: 124 VEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRFEIK 183 Query: 192 ALQRKLGITFVFVTHDQEEALTMSDRIVVM-RDGRIEQDGTPREIYEEPKNLFVAGFIGE 250 LQR LGIT ++VTHDQE AL +SDR+ +M G I Q GTP EI+E P + FV F+G Sbjct: 184 ELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFRFMGV 243 Query: 251 INMFNATVIERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVL--LRPEDLRVEEINDDN 308 N A R + A E V + + G H + RP D+R+ D Sbjct: 244 ANFLPA---RRRGMAMLAAGGEQP-----VPWGLPDGDAEHWMAGFRPSDVRLARQGD-- 293 Query: 309 HAEGLIGYVRERNYKGMTLESVVELE 334 GL G VR ++ G + ++E++ Sbjct: 294 ---GLRGTVRRASFLGAMTDYLIEVD 316 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: 305 Number of extensions: 14 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: 366 Length adjustment: 30 Effective length of query: 348 Effective length of database: 336 Effective search space: 116928 Effective search space used: 116928 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