Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate H281DRAFT_00169 H281DRAFT_00169 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Burk376:H281DRAFT_00169 Length = 371 Score = 417 bits (1073), Expect = e-121 Identities = 225/371 (60%), Positives = 277/371 (74%), Gaps = 7/371 (1%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 MA+L +R+V KTY G+P LK + + I++G+FLILVG SGCGKSTL+N IAGLET+T G Sbjct: 1 MASLSIRDVYKTYPNGVP-VLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKG 59 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 I I + V+ +SPKDRDIAMVFQSYALYP+M+VRENI FGL IRK+P+ + V RV+ Sbjct: 60 EIQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRKVPKQEQAQIVDRVS 119 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 LQI HLL+RKPGQLSGGQ+QRVAMGRALAR P ++LFDEPLSNLDAKLR+EMR+E+KL Sbjct: 120 NTLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRSEIKL 179 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +HQRL TT VYVTHDQIEAMTLGD++AVMKDGI+QQFG P+EIY++P+N FVA FIG+PP Sbjct: 180 LHQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGFIGAPP 239 Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLED---RDVILGLRPEQIMLAAG- 296 MNF+ +L + + LD+G R L L A ++ R+VILGLRPE+I A G Sbjct: 240 MNFIQGKLVEQGAGVGIELDTGVTRTALNLPFDSAKVKSHVGREVILGLRPERITDARGA 299 Query: 297 EGDSA--SSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKV 354 GD A I +V V EPTGPDTLVF Q+N +V R+ P PQ TL FD SK Sbjct: 300 HGDHARLQQIEVKVDVIEPTGPDTLVFAQVNGKRVVSRVHPASNPQPLTNTTLLFDTSKA 359 Query: 355 LLFDANTGERL 365 +LFD + ER+ Sbjct: 360 VLFDPSNEERI 370 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: 442 Number of extensions: 16 Number of successful extensions: 4 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: 371 Length adjustment: 30 Effective length of query: 356 Effective length of database: 341 Effective search space: 121396 Effective search space used: 121396 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