Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__Phaeo:GFF262 Length = 348 Score = 255 bits (652), Expect = 1e-72 Identities = 128/244 (52%), Positives = 177/244 (72%), Gaps = 3/244 (1%) Query: 18 VQLAGIRKCF-DGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIML 76 V L +RK + +G E + I +GEF+ L+GPSGCGK+T+LR+IAGLE + G + + Sbjct: 4 VTLNSVRKVYPNGVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEGTLEI 63 Query: 77 DNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQ 136 + + +V +R + VFQ+YAL+PHMTV +N+A+GL+ +KTP AEI +V EA +M+ Sbjct: 64 GDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAAKMLN 123 Query: 137 LETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRK 196 LE + RKP QLSGGQ+QRVA+ RA+V P L L DE LS LD KLR QM+ E+KALQR+ Sbjct: 124 LEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKALQRR 183 Query: 197 LGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIG--EINMF 254 LG+T ++VTHDQ EA+TM+DRI+V+ GRIEQ GTP EIY P ++FVA F+G +N+ Sbjct: 184 LGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPPMNLL 243 Query: 255 NATV 258 +AT+ Sbjct: 244 DATI 247 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: 329 Number of extensions: 8 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: 348 Length adjustment: 29 Effective length of query: 349 Effective length of database: 319 Effective search space: 111331 Effective search space used: 111331 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