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::Q8NMV1 (376 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 224 bits (572), Expect = 2e-63 Identities = 123/298 (41%), Positives = 183/298 (61%), Gaps = 23/298 (7%) Query: 26 LEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQN 85 L+I GEFL ++GPSGCGK+T LR+LAG E+ + G I + + + V P R + VFQ+ Sbjct: 28 LDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIILDGRSMRDVPPDGRRVNTVFQS 87 Query: 86 YALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQRQRVA 145 YAL+PHM+V +N+ F L+++G + EI +RV +A +GL R+P +LSGGQ+QRVA Sbjct: 88 YALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMVGLAGQAGRRPTSLSGGQQQRVA 147 Query: 146 MGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALTMGDR 205 + RA+V P V L+DEPLS LD KLRVQ RT++ L+R++G+T ++VTHDQ EA +M DR Sbjct: 148 IARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRREMGITFIFVTHDQEEAFSMSDR 207 Query: 206 IAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGD-----------AT 254 + V+ +G + QVG P E+Y++P N+FVA F+G + G DG Sbjct: 208 VVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGETNVFEGVAGQSDGGILQALVEGRTCEL 267 Query: 255 SGH--------ARIKLSPETLAA--MTPEDNGRITIGFRPEALEIIPEGESTDLSIPI 302 S H R+ L PE L PED+ ++ + R +E + +G + D+ + + Sbjct: 268 SSHRGFQPGDRIRVLLRPEDLLVEREEPEDDDKLWLPGR--IMETVYKGSTWDMVVQL 323 Lambda K H 0.316 0.135 0.380 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: 16 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: 376 Length of database: 370 Length adjustment: 30 Effective length of query: 346 Effective length of database: 340 Effective search space: 117640 Effective search space used: 117640 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 (21.6 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