Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >NCBI__GCF_002019605.1:WP_078429421.1 Length = 351 Score = 234 bits (596), Expect = 4e-66 Identities = 141/338 (41%), Positives = 198/338 (58%), Gaps = 40/338 (11%) Query: 20 LEIRNLTKSYD--GQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIM 77 ++ N+TK Y+ AVD ++L I +GEI LLG SGCGK+T LRMLAGFEQP+ G+I Sbjct: 4 IQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTGKIR 63 Query: 78 L-DGV---DLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEM 133 + D V D +PP R I M+FQ YALFPH+T+E+N+ FGL + K + R E+ Sbjct: 64 IGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRWK--NRDKKKRAQEV 121 Query: 134 LGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVV 193 L LV + EF R P +LSGGQ+QRVALAR+LA RPK++L+DEP LD LR++M+ +V Sbjct: 122 LELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRYDVT 181 Query: 194 DILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSV 253 +IL + T ++VTHDQ++A ++ R+ +MN G QI P+E+Y P + A+F+G Sbjct: 182 NILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFVGKT 241 Query: 254 NVFEGVLKERQEDGLVLDSPGLVH----------PLKVDADASVVDNVPVHVALRPEKIM 303 N+ G L P L H P + D V++N V V++RPE Sbjct: 242 NLISGTL-----------CPDLKHVETHIGRVCLPQETD---KVIEN--VMVSIRPEGCR 285 Query: 304 LCEEPPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQM 341 L E+ G V + Y G+ HVRL+S Q+ Sbjct: 286 LAEK------GRYAGLVERVTYSGEYQEVHVRLQSDQV 317 Lambda K H 0.321 0.137 0.400 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: 17 Number of successful extensions: 4 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: 377 Length of database: 351 Length adjustment: 29 Effective length of query: 348 Effective length of database: 322 Effective search space: 112056 Effective search space used: 112056 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