Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate BPHYT_RS35680 BPHYT_RS35680 sugar ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__BFirm:BPHYT_RS35680 Length = 360 Score = 315 bits (808), Expect = 1e-90 Identities = 173/366 (47%), Positives = 233/366 (63%), Gaps = 8/366 (2%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 MA ++L + K YG + I+L I +GEF++LVGPSGCGKSTLM +AGLE I+GG Sbjct: 1 MAAVQLSGIFKRYGD--TQVVHGIDLDIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 +MIG + ++P+ R+I+MVFQSYALYP +SV ENI FG +IRK A + A Sbjct: 59 DLMIGGTRANSLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESSASFKPRIEAAA 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 K+L + L+R P LSGGQ+QRVAMGRA+ R P ++LFDEPLSNLDAKLRV+MRTE+K Sbjct: 119 KMLNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKA 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +HQRLK T +YVTHDQIEAMT+ D++ VM G I+Q G P E+Y++PAN FVASF+GSP Sbjct: 179 LHQRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPS 238 Query: 241 MNFVP-LRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGD 299 MNF + R G+ +AL +G L + + V LG+RPE I D Sbjct: 239 MNFAEGVIASRAQGQGLALNLTGGGEIVLE-GAPASAVVGAKVTLGVRPEHIETMTPTPD 297 Query: 300 SASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDA 359 + EV+V EPTG +T ++ ++ + C + G+ +TL+ + LFD Sbjct: 298 AT----MEVEVVEPTGAETHLYGKIGGSTWCVTTRQRSKIEPGQRVTLRLPAEHIHLFDT 353 Query: 360 NTGERL 365 +G RL Sbjct: 354 ESGRRL 359 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: 387 Number of extensions: 14 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: 360 Length adjustment: 30 Effective length of query: 356 Effective length of database: 330 Effective search space: 117480 Effective search space used: 117480 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