Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_011974130.1 MAEO_RS07290 ATP-binding cassette domain-containing protein
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_000017185.1:WP_011974130.1 Length = 373 Score = 157 bits (396), Expect = 6e-43 Identities = 102/304 (33%), Positives = 169/304 (55%), Gaps = 22/304 (7%) Query: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 LE++N+ K TL+ L+IK+ ++ I +G SG GK+TL+ +AG G I+ Sbjct: 2 LEIKNLKKKLN---DFTLEIDNLTIKDDDYFIFLGLSGSGKTTLLEIMAGFSKADSGTIL 58 Query: 64 IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123 + +D++ R+IA+ Y L+P +++ +NIE G+K I+ + +AK L Sbjct: 59 LDGKDITNKPINKRNIALCNGKY-LFPHLTISKNIELGIKNNSNKNDKIEI-IENIAKTL 116 Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMK-LMH 182 +I+HLLNR P LS G++QRV++ ALA P+I L DEPLS+LD + E+ E++ + H Sbjct: 117 KIKHLLNRYPKNLSMGERQRVSLAMALAMEPRIILLDEPLSSLDRLIHEELLYELREIYH 176 Query: 183 QRLKTTT--VYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 TTT ++VTHD EA+ L + +A++ G I+Q G KEI P ++FVA F G Sbjct: 177 NSNNTTTTIIHVTHDFNEAIALSNNIAILNKGKIEQMGNIKEILRYPKSEFVAKFTGL-- 234 Query: 241 MNFVPLRLQR-----------KDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPE 289 N + R+ + K+ + L+ R ++ ++ + + +LG+RPE Sbjct: 235 RNLLNGRVIKQLNENEEIYLFKNENITIQLNGNDKRITKFIDNSKNQIY-KKALLGVRPE 293 Query: 290 QIML 293 +IM+ Sbjct: 294 EIMI 297 Lambda K H 0.318 0.135 0.382 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: 290 Number of extensions: 15 Number of successful extensions: 5 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: 386 Length of database: 373 Length adjustment: 30 Effective length of query: 356 Effective length of database: 343 Effective search space: 122108 Effective search space used: 122108 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 (21.7 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