Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 239 bits (610), Expect = 9e-68 Identities = 141/342 (41%), Positives = 203/342 (59%), Gaps = 19/342 (5%) Query: 4 LKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELD 63 L + N+ K F ++ +L + D EF +GPSGCGK+T+LRLIAG E+ + G I L+ Sbjct: 7 LTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLN 66 Query: 64 GRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARILEL 123 G DI + KR VFQ+YAL+PH++V N++F L +AGV ++ +V++A I+ L Sbjct: 67 GDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRL 126 Query: 124 GPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKEL 183 RKP QLSGGQ+QRVAI RA+V PKI L DE LS LD LR QM+LEL +L ++L Sbjct: 127 SEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQL 186 Query: 184 QATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMGFLK 243 T +YVTHDQ EA++M+D+++V++ G+ +QVG+P ++Y P NLFVA F+G ++ Sbjct: 187 GITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIG--EINVFD 244 Query: 244 GKITRVDSQGCEVQLDAGTR--VSLPLGGRHLSVGSAVTLGIRPEHLELAKPGDCALQVT 301 G+I V + G E Q +A V +VG V + +RPE L + DC Sbjct: 245 GEI--VQALG-EYQYEASINGVVREIRCDHRFAVGDKVHVMLRPEDLRI----DC----R 293 Query: 302 ADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLH 343 DV+ER G R+ +G+ L + G+TL H Sbjct: 294 PDVAERKGFPGIVLERSYTGQTLNSHIE----LENGQTLMAH 331 Lambda K H 0.320 0.137 0.389 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: 320 Number of extensions: 11 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: 367 Length of database: 369 Length adjustment: 30 Effective length of query: 337 Effective length of database: 339 Effective search space: 114243 Effective search space used: 114243 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