Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1302 (334 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 228 bits (582), Expect = 1e-64 Identities = 125/273 (45%), Positives = 169/273 (61%), Gaps = 4/273 (1%) Query: 4 IKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRID 63 I+ E ++K FG + +DL I GEF +G SGCGK+TLLR++AG E T+G I ID Sbjct: 23 IRFEGISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILID 82 Query: 64 GEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAALNL 123 G+D T +PP +R + M+FQSYAL+PHMSV NIAF +K G+ K ++ A + + Sbjct: 83 GQDVTEVPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELVQM 142 Query: 124 TDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRL 183 + R+P QLSGGQRQRVA+ R + +EP L DEPL+ LD LR +LE+ + R+ Sbjct: 143 GRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQDRV 202 Query: 184 ATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMNLLT 243 T + VTHDQ EAMTM+ +I V+ AG IEQVGSP+++Y P FVA FIG+ N+ Sbjct: 203 GITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIGA--ANMFQ 260 Query: 244 GPQAAQHNAATIGI-RPEH-LSISETEGMWAGT 274 G A I EH LS++E + AGT Sbjct: 261 GSVRGGEGALAIACPELEHDLSVTEAGAVAAGT 293 Lambda K H 0.320 0.138 0.400 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: 298 Number of extensions: 13 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: 334 Length of database: 379 Length adjustment: 29 Effective length of query: 305 Effective length of database: 350 Effective search space: 106750 Effective search space used: 106750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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