Align LacF, component of Lactose porter (characterized)
to candidate WP_012758788.1 RLEG_RS16915 sugar ABC transporter permease
Query= TCDB::P29823 (298 letters) >NCBI__GCF_000023185.1:WP_012758788.1 Length = 307 Score = 164 bits (416), Expect = 2e-45 Identities = 98/295 (33%), Positives = 161/295 (54%), Gaps = 14/295 (4%) Query: 8 SLKRYYDVNGWLFVAPAIALISVFMLYPILRSLVLSL--YTGRGMMLKFSGTGNLVR-LW 64 +LK + WLFV+P + +F L P+ + S+ + F G N L+ Sbjct: 18 TLKMREMMEAWLFVSPTLIGFLIFFLGPLCAVVYYSMTEWNLLSQQATFVGLANFQNALF 77 Query: 65 NDPVFWQALQNTVIFFVVQVPIMITMALILAAMLNNPKLRYSGL--FRTMIFLPCVSSLV 122 +P FW ++N+VIF + VP+ + +AL LA L+ P + G+ FRT+ F P ++S + Sbjct: 78 ENPDFWLVVRNSVIFAIGLVPLNMALALALALALSRP---FFGVVFFRTVFFAPVITSAI 134 Query: 123 AYSILFKSMFSLDG-VVNNTLLAIGIIGEPIGWLTDPFWAKVLIIIAITWRWTGYNMIFY 181 A++I++K + +G +N L +GI G WL +P WA +I+ + G NMI Y Sbjct: 135 AWAIVWKFLLQGEGGFINQVLALVGITGP--NWLREPSWAMAAVIVTRVIKMVGLNMILY 192 Query: 182 LAALQNIDRSIYEAAKIDGVPSWGRFAFLTIPMLKPVILFTTITSTIGTLQLFDEVYNFT 241 +AALQ I R EAA+++G F+ +T P+L P L + +TIG+ ++FD +Y T Sbjct: 193 IAALQAIPRDYEEAARLEGASRRQIFSMITWPLLAPTTLVIMVITTIGSFKVFDHIYQMT 252 Query: 242 EGTGGPANSTLTLSLYIYNLTFRFMPSFSYAATVSYVIVLMVAVLSFLQFYAARE 296 GGP N TL L+ YIY F+F + YA+ ++ ++ +M+ L+ +Q R+ Sbjct: 253 --GGGPENGTLVLAFYIYQQGFKFF-NVGYASALAMIMFVMIMALTLVQVMLRRK 304 Lambda K H 0.329 0.141 0.435 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: 257 Number of extensions: 15 Number of successful extensions: 5 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: 298 Length of database: 307 Length adjustment: 27 Effective length of query: 271 Effective length of database: 280 Effective search space: 75880 Effective search space used: 75880 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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