Align LacK, component of Lactose porter (characterized)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= TCDB::Q01937 (363 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 296 bits (757), Expect = 7e-85 Identities = 165/356 (46%), Positives = 224/356 (62%), Gaps = 19/356 (5%) Query: 6 LTDIRKSYG----SLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGELT 61 + I K +G S+EV++ V++ V+ GEF++ VGPSGCGKSTLL +IAGL++ + GE+ Sbjct: 7 IAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIR 66 Query: 62 IGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKIL 121 IGG + + P R IAMVFQ+YALYP ++V +N+GFAL M K E ++R++ A +L Sbjct: 67 IGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAML 126 Query: 122 ELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLHK 181 ++ L+DR+P LSGGQRQRVA+GRA+ RQP +FLFDEPLSNLDA+LRV MR EI RLH+ Sbjct: 127 QISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQ 186 Query: 182 ELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMNF 241 T VYVTHDQVEAMTL +I VM+GG+V+Q+G P +Y+ P N +VA FIGSP MN Sbjct: 187 ASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNL 246 Query: 242 LPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDTQLT 301 L V G G Q AL P PP + V +GVRPEH + + + Sbjct: 247 LRGAVTGGQFGIQ-GAALNLAP----------PPSSANEVLLGVRPEHLVMQETAPWR-- 293 Query: 302 AHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLFDA 357 V VVE G +YV T G + + R + G+ + + ++ + FDA Sbjct: 294 GRVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTR--VQPGEHVGLALAPAHAHWFDA 347 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: 366 Number of extensions: 9 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: 363 Length of database: 355 Length adjustment: 29 Effective length of query: 334 Effective length of database: 326 Effective search space: 108884 Effective search space used: 108884 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