Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 219 bits (559), Expect = 7e-62 Identities = 127/315 (40%), Positives = 183/315 (58%), Gaps = 19/315 (6%) Query: 4 VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63 + + ++ F TVL + LDI HGEFL +LG SGCGK+TLL +AG S G+I + Sbjct: 8 IRLEHVAKEFDGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIILD 67 Query: 64 DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123 R++ P R + VFQSYAL+P M+V N++FGL+++ IP EI +RV +A ++ + Sbjct: 68 GRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMVGL 127 Query: 124 QPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSL 183 R+P+ LSGGQ+QRVAI RA+V V L DEPLS LD KLR ++R E+K+L + + Sbjct: 128 AGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRREM 187 Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFR 243 T I+VTHDQ EA +++DR+ VM G + Q+ P+ +Y P N+FVA F+G N F Sbjct: 188 GITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVG--ETNVFE 245 Query: 244 GEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTHQAV 303 G DG + + +H QPG ++ + LRPE + + Sbjct: 246 GVAGQSDGG--ILQALVEGRTCELSSHRGFQPGDRIRVLLRPEDL--------------L 289 Query: 304 VDIEEPMGADNLLWL 318 V+ EEP D+ LWL Sbjct: 290 VEREEPED-DDKLWL 303 Lambda K H 0.320 0.137 0.392 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: 376 Number of extensions: 21 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: 361 Length of database: 370 Length adjustment: 30 Effective length of query: 331 Effective length of database: 340 Effective search space: 112540 Effective search space used: 112540 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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