Align LacK, component of Lactose porter (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= TCDB::Q01937 (363 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 229 bits (585), Expect = 7e-65 Identities = 132/339 (38%), Positives = 196/339 (57%), Gaps = 13/339 (3%) Query: 4 VRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGELTIG 63 +R I K +G ++ V+L + GEF +G SGCGK+TLLRM+AG E ++G + I Sbjct: 23 IRFEGISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILID 82 Query: 64 GTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKILEL 123 G + +V P +R + M+FQ+YAL+PHM+V +N+ F L+ G+AK I+ +V AA +++++ Sbjct: 83 GQDVTEVPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELVQM 142 Query: 124 DALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLHKEL 183 RKP LSGGQRQRVA+ R + ++P V L DEPL+ LD +LR ++E+ + + Sbjct: 143 GRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQDRV 202 Query: 184 NATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMNFLP 243 T V VTHDQ EAMT++ +I VM G +EQVG+P+ +Y+ P FVA FIG+ M Sbjct: 203 GITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIGAANM---- 258 Query: 244 AVVIGQAEGGQVTVALKARPDTQ--LTVACATPPQGGDAVTVGVRPEHFLPA----GSGD 297 G GG+ +A+ A P+ + L+V A G VTV VRPE + A SG Sbjct: 259 --FQGSVRGGEGALAI-ACPELEHDLSVTEAGAVAAGTPVTVMVRPEKVMIARDKPASGL 315 Query: 298 TQLTAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHG 336 V + +LG+ S + G +I + HG Sbjct: 316 NWAEGVVSDIAYLGDVSIYHVRLASGRKIQALRTNLHHG 354 Lambda K H 0.320 0.137 0.390 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: 309 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: 363 Length of database: 379 Length adjustment: 30 Effective length of query: 333 Effective length of database: 349 Effective search space: 116217 Effective search space used: 116217 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