Align LacK, component of Lactose porter (characterized)
to candidate Ac3H11_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q01937 (363 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2058 Length = 360 Score = 239 bits (610), Expect = 8e-68 Identities = 144/350 (41%), Positives = 202/350 (57%), Gaps = 18/350 (5%) Query: 2 AEVRLTDIRKSYGSLE----VIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISS 57 A + +I K YG+ +KG++ EV G +GPSGCGK+T LRMIAGLE +S Sbjct: 6 AGIVFRNITKRYGTDSSAALAVKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGLESPTS 65 Query: 58 GELTIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAA 117 GE+ IGG + + P++R ++M+FQ+YAL+PHM V EN+ + LR +G K++ + A Sbjct: 66 GEIFIGGKDVTTLGPAQRNVSMMFQSYALFPHMNVVENVMYGLRMSGQPKEQARAKAVEA 125 Query: 118 AKILELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIA 177 + + L DR P LSGGQ+QRVA+ RA+V +P+V LFDEPLSNLDA LR MR EI Sbjct: 126 LRGVGLVGFDDRLPSELSGGQQQRVALARALVLEPEVLLFDEPLSNLDARLRREMREEIR 185 Query: 178 RLHKELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSP 237 L + L+ T+ YVTHDQ EAM ++D+I+VM G++ Q G+P ALY+ P + FVAGF+G Sbjct: 186 ALQQRLSLTVAYVTHDQAEAMAVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAGFMGEA 245 Query: 238 RMNFLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGD 297 + PAV A+G L RP VA + P V V VRPE + G+ Sbjct: 246 ML--FPAV--ADADGTVALGPLVLRP----RVAVKSGP-----VKVAVRPEAWRITRQGE 292 Query: 298 TQLTAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGI 347 L A + +LG T G I + + GD++ +G+ Sbjct: 293 GLLPARLAKSAYLGAVHEYTFETALG-SIFVVSSDLDDVLAVGDDVQLGL 341 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: 350 Number of extensions: 17 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: 360 Length adjustment: 29 Effective length of query: 334 Effective length of database: 331 Effective search space: 110554 Effective search space used: 110554 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