Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate GFF1915 PGA1_c19470 ABC transporter, ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Phaeo:GFF1915 Length = 363 Score = 319 bits (818), Expect = 7e-92 Identities = 165/350 (47%), Positives = 234/350 (66%), Gaps = 9/350 (2%) Query: 16 GLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIMIGDQDVSGMSPK 75 G + LK++ L I++GEFL+L+G SGCGKSTL+N IAGL+ T G I I D++V+ PK Sbjct: 23 GAVEVLKSLNLDIQKGEFLVLLGASGCGKSTLLNTIAGLQEATEGQIWINDENVTWREPK 82 Query: 76 DRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLLQIEHLLNRKPGQ 135 DR +AMVFQSYALYP M+VR N+ FGL++ K+P+A+ D V A++LQ+E LL+R+PG+ Sbjct: 83 DRGLAMVFQSYALYPKMTVRGNLAFGLRMNKVPKAEADKLVDEAARVLQLEELLDRRPGE 142 Query: 136 LSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHD 195 LSGGQ+QRVA+GRAL R+ ++LFDEPLSNLDAKLR E+R E+K +HQ L T +YVTHD Sbjct: 143 LSGGQRQRVAIGRALVRKVDVFLFDEPLSNLDAKLRAELRVELKRLHQELGATMIYVTHD 202 Query: 196 QIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNFVPLRLQRKDGRL 255 Q+EA+TL D++AVMKDG++QQ +P+EIY PAN++VA F+G P MNFV + Sbjct: 203 QVEALTLADRIAVMKDGVVQQLDSPEEIYRRPANRYVAQFVGLPSMNFVNGVVTESGAIQ 262 Query: 256 VALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDSASSIRAEVQVTEPTG 315 + +C LA +T G E V +G+RPE + A +A +V + E G Sbjct: 263 TEDFELALDQCNLA-STPAPGTE---VEIGIRPEHVHPA-----NAGGFMLDVGMVELLG 313 Query: 316 PDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDANTGERL 365 + L++ ++ +T + R PD + G+ + + P +F A TG R+ Sbjct: 314 SERLIWGKVGNTSIVMRDDPDTTIRSGDQVRINLKPGAFSVFSAKTGLRI 363 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: 339 Number of extensions: 12 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: 386 Length of database: 363 Length adjustment: 30 Effective length of query: 356 Effective length of database: 333 Effective search space: 118548 Effective search space used: 118548 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 Sep 17 2021. 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