Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= TCDB::Q97Q42 (385 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 205 bits (521), Expect = 2e-57 Identities = 132/362 (36%), Positives = 199/362 (54%), Gaps = 38/362 (10%) Query: 22 VLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTGDIMLDGVRINDIPTNKRDV 81 VL IN E+ +G+F ++G SG GKST+L ++AGL + G I + R++ +P RD+ Sbjct: 49 VLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAKARDI 108 Query: 82 HTVFQSYALFPHMNVFENVAFPLR---------------LRKIDKK---------EIEQR 117 VFQSYAL+PH++V++N+AF LR R + K I++R Sbjct: 109 AMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEARIKRR 168 Query: 118 VAEVLKMVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQ 177 V EV M+QL+ R ++LSGGQ+QRVA+ RAI P+V L+DEPLS LD KLR + + Sbjct: 169 VREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLRAETR 228 Query: 178 YELRELQQRLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATF 237 ++ LQ++LG+T ++VTHDQ EA+ M D I V+N G + Q +P++IYD P N FVA F Sbjct: 229 AQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRFVAQF 288 Query: 238 IGE--SNILPGTM---IEDYLVEFNGKRFEAVDGGMK--PNEPVEVVIRPEDLRITLPEE 290 IG N++P T+ ++ F EA + ++ + VE+ IRPE L + Sbjct: 289 IGSPPMNLIPVTVRAPLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPEHLEVGAAAS 348 Query: 291 GKLQVKVDTQLFRGVHYEIIAYDELGNEWMIHSTRKA-----IVGEEIGLDFEPEDIHIM 345 L + V + + EL + R A +G+ + L F+P+ IH+ Sbjct: 349 KNLLITVTG--VEALGSDTFIAGELKESGIAVQARLAPQQCWQMGDRLWLTFKPDQIHLF 406 Query: 346 RL 347 L Sbjct: 407 DL 408 Lambda K H 0.318 0.138 0.386 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: 339 Number of extensions: 12 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: 385 Length of database: 417 Length adjustment: 31 Effective length of query: 354 Effective length of database: 386 Effective search space: 136644 Effective search space used: 136644 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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