Align LacF, component of Lactose porter (characterized)
to candidate N515DRAFT_3134 N515DRAFT_3134 multiple sugar transport system permease protein
Query= TCDB::P29823 (298 letters) >FitnessBrowser__Dyella79:N515DRAFT_3134 Length = 292 Score = 182 bits (461), Expect = 1e-50 Identities = 108/285 (37%), Positives = 163/285 (57%), Gaps = 11/285 (3%) Query: 18 WLFVAPAIALISVFMLYPILRSLVLSL-----YTGRGMM-LKFSGTGNLVRLWNDPVFWQ 71 WLF+APA+ ++ +F L P++ +L LSL Y + L+F GN L + P+FW Sbjct: 8 WLFLAPALLVLGLFFLLPVIAALALSLTDYDLYALADIRDLRFVALGNYWELLHRPLFWS 67 Query: 72 ALQNTVIFFVVQVPIMITMALILAAMLNNPKLRYSGLFRTMIFLPCVSSLVAYSILFKSM 131 AL +T+ F +V VP+ I +L A +LN+P R LFRT +F P V+++VA +++++ + Sbjct: 68 ALGHTLYFVLVGVPLSIVASLGAALLLNSPLARCKPLFRTALFAPVVTTVVAVAVIWRYL 127 Query: 132 FSLD-GVVNNTLLAIGIIGEPIGWLTDPFWAKVLIIIAITWRWTGYNMIFYLAALQNIDR 190 F+ G+ N L +GI P+ WL DP WA II+ W+ GYNMI +LAALQ I Sbjct: 128 FNTKYGLANYALGGLGI--HPVDWLGDPRWAMPTIILFAVWKNFGYNMIIFLAALQAIPA 185 Query: 191 SIYEAAKIDGVPSWGRFAFLTIPMLKPVILFTTITSTIGTLQLFDEVYNFTEGTGGPANS 250 +YEAA+IDG +F +T+PML P +L I + G QLF E + TE GGP S Sbjct: 186 DLYEAARIDGASPLRQFRHITLPMLGPTLLMVGILTVSGYFQLFAEPFVMTE--GGPLQS 243 Query: 251 TLTLSLYIYNLTFRFMPSFSYAATVSYVIVLMVAVLSFLQFYAAR 295 T ++ +Y F++ S +A + ++M AV + + A R Sbjct: 244 TTSVLYLMYEEGFKWWNLGSASAVAFLLFLIMFAVTAVMLRVARR 288 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: 266 Number of extensions: 14 Number of successful extensions: 3 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: 292 Length adjustment: 26 Effective length of query: 272 Effective length of database: 266 Effective search space: 72352 Effective search space used: 72352 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 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