Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)
Query= TCDB::Q97Q42 (385 letters) >FitnessBrowser__Miya:8500851 Length = 354 Score = 214 bits (544), Expect = 4e-60 Identities = 136/353 (38%), Positives = 199/353 (56%), Gaps = 33/353 (9%) Query: 6 IEFKNVSKVFEDSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTGDI- 64 + NV+K F + +N E+ G+ +++LG SG GK+T L ++AG D G+I Sbjct: 4 VRLVNVTKRF--GGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGEIH 61 Query: 65 ----MLDGVRIND-IPTNKRDVHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQRVA 119 +L R N +P KRD VFQ++A++PH++V+ENVAFPLR+R++ EI++R Sbjct: 62 VGDRLLSARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRRTR 121 Query: 120 EVLKMVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYE 179 E L L ++S LSGG +QRVA+ARA+ P V+LLDEPLS+LD LR +M++E Sbjct: 122 EALHHTSLADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMRFE 181 Query: 180 LRELQQRLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATFIG 239 +++LQ+ G + ++VTHDQ EA+A+SD I VM +G + Q GTP+D+Y P N FV FIG Sbjct: 182 IKDLQRTFGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFGFIG 241 Query: 240 ESNILPGTMIEDYLVEFNGKRFEAVDGGMKPNEP----------VEVVIRPEDLRITLPE 289 SN L + + LV NG D + P P + RP ++ T Sbjct: 242 LSNFLDVNLTPEGLVRVNGG-----DARVTPATPPSARLVSAGRAALASRPSEIDFT--A 294 Query: 290 EGKLQVKVDTQLFRGVHYEIIAY--DELGNEWMIHSTRKA---IVGEEIGLDF 337 EG L+ V + + G EI+ Y D G E + R+A G+ GL F Sbjct: 295 EGGLRGVVRRRAYLG---EIVDYRIDVSGQEVRVQKGRRAPGPAEGDACGLVF 344 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: 291 Number of extensions: 11 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: 385 Length of database: 354 Length adjustment: 30 Effective length of query: 355 Effective length of database: 324 Effective search space: 115020 Effective search space used: 115020 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: 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