Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 182 bits (463), Expect = 9e-51 Identities = 110/309 (35%), Positives = 181/309 (58%), Gaps = 22/309 (7%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 M+TL ++ ++ Y L+ + L++ +GE L+GPSGCGK+TL+ IAGL+ I+ G Sbjct: 1 MSTLSIQGLHSDYRG--EQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAG 58 Query: 61 AIMIGDQDVSG----MSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEV 116 +I I + VS ++P+ R I M+FQ YAL+P ++V +NI FG +R++ + + Sbjct: 59 SIAINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFG--VRQLDKQSRSVRL 116 Query: 117 ARVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176 + L+++E L R P +LSGGQQQRV++ RALA P + L DEP SN+DA++R + Sbjct: 117 EEMLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALML 176 Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFI 236 E++ + + + V+VTH + EA D +A+ + G I Q G P+ +Y +P +VA F+ Sbjct: 177 EIRAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFL 236 Query: 237 GSPPMNFVPLRLQRKDGRLVALLDSGQARCEL-ALNTTEAGLEDRDVILGLRPEQIMLAA 295 G+ N++ +RL+ G+L++ L + + A + T L LRPEQ+++ A Sbjct: 237 GA--SNYLDVRLEA--GQLISTLGAFPLPQDFKAASETGRWL--------LRPEQLLIEA 284 Query: 296 GEGDSASSI 304 D A I Sbjct: 285 -RADGAGEI 292 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: 272 Number of extensions: 9 Number of successful extensions: 3 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: 341 Length adjustment: 29 Effective length of query: 357 Effective length of database: 312 Effective search space: 111384 Effective search space used: 111384 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 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