Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein (TIGR)
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__DvH:208681 Length = 349 Score = 274 bits (701), Expect = 2e-78 Identities = 156/367 (42%), Positives = 221/367 (60%), Gaps = 19/367 (5%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 M+T+ L V++ +G + ++ +++G+ L+L+GPSGCGKST + IAGLE++T G Sbjct: 1 MSTIVLDKVSRHWGD--VRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 I+IG +DV+ + P R +AMVFQSYAL+P ++VR+NI FGL +RK+P A+ + R Sbjct: 59 RILIGGRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRLDRAV 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++L + LL RKPG+LSGGQQQRVA+GRAL + L DEPLSNLDAKLR EMR E++ Sbjct: 119 EILGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIRA 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 + Q L T VYVTHDQ EAM++ D++ +M+ G I Q TP E+Y+ PA F SFIG+PP Sbjct: 179 LQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGTPP 238 Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 MN V L+ DG VA SG+ C D +LG+RPE I + Sbjct: 239 MNLVRLQ-GNDDGIRVAGSRSGRVTCHAG----------ADCMLGIRPEHIRIV------ 281 Query: 301 ASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDAN 360 RA V+ E G ++++ ++ ++ + VG + L V +FDA Sbjct: 282 DDGWRAVVESVEYLGSNSVLSCRVGSEELSVVVHGVTDTVVGAEIYLHCPEEHVHIFDAA 341 Query: 361 TGERLGT 367 TG R T Sbjct: 342 TGARHAT 348 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: 309 Number of extensions: 11 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: 386 Length of database: 349 Length adjustment: 30 Effective length of query: 356 Effective length of database: 319 Effective search space: 113564 Effective search space used: 113564 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: 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