Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 246 bits (627), Expect = 1e-69 Identities = 143/361 (39%), Positives = 218/361 (60%), Gaps = 19/361 (5%) Query: 18 VQLAGIRKCFDG--KEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIM 75 ++L IRK + G +E + +D+ I +GEFL L+GPSGCGK+T++ IAGLET+ G I+ Sbjct: 4 LELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDGSIV 63 Query: 76 LDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMV 135 LD +DI+ + ++R + VFQSYAL+P M+V EN+AFGL+++ P EI V ++ Sbjct: 64 LDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVADLL 123 Query: 136 QLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQR 195 Q+ +KP LSGGQQQRVA+ RA+ +PR+ L DE LS LD KLR +M+ E+K L + Sbjct: 124 QISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKKLHQ 183 Query: 196 KLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFN 255 +L T V+VTHDQ EA+T++DRI V++DG ++Q GTP+E+Y+ P+NLFVAGF+G M Sbjct: 184 RLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPAMSF 243 Query: 256 ATVIERLDEQRVRANV---EGRECNIYVN--FAVEPGQKLHVLLRPEDLRVEEINDDNHA 310 V E ++A V +GR + V A G+K+ + +RPE + + D + Sbjct: 244 VPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPE--HITQPQDQKND 301 Query: 311 EGLIGYVRERNYKGMTLESVVELENGKMVMVSEFFNEDDPDFDHSLDQKMAINWVESWEV 370 + L+ KG E +E+ V +D + +D + + W E+ E+ Sbjct: 302 QTLVA-------KG---EFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAEL 351 Query: 371 V 371 + Sbjct: 352 M 352 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: 345 Number of extensions: 13 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: 372 Length adjustment: 30 Effective length of query: 348 Effective length of database: 342 Effective search space: 119016 Effective search space used: 119016 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