Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 246 bits (627), Expect = 1e-69 Identities = 136/293 (46%), Positives = 184/293 (62%), Gaps = 15/293 (5%) Query: 4 VLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLY 63 + LEH+ K + G+T + D LDI+ EF +GPSGCGKTT LR++AG E + G + Sbjct: 8 IRLEHVAKEFDGET--VLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEII 65 Query: 64 IGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKIL 123 + R + DVPP R + VFQ+YAL+PHM+V+ N+AFGL++ +PK EI RV +A +++ Sbjct: 66 LDGRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMV 125 Query: 124 DIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQ 183 +A R+P +LSGGQ+QRVA+ RA+V P V L+DEPLS LD KLRVQMR E+++L + Sbjct: 126 GLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRR 185 Query: 184 RLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNF 243 + T I+VTHDQ EA +M DR+VVM +G + Q TP VY QP NMFVA F+G N Sbjct: 186 EMGITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGE--TNV 243 Query: 244 IRGEIVQ-DGDAFYFRAPSISLRLPEGRYGVLKASGAI--GKPVVLGVRPEDL 293 G Q DG I L EGR L + G + + +RPEDL Sbjct: 244 FEGVAGQSDG--------GILQALVEGRTCELSSHRGFQPGDRIRVLLRPEDL 288 Lambda K H 0.321 0.138 0.395 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: 392 Number of extensions: 18 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: 384 Length of database: 370 Length adjustment: 30 Effective length of query: 354 Effective length of database: 340 Effective search space: 120360 Effective search space used: 120360 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: 50 (23.9 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