Align LacF, component of Lactose porter (characterized)
to candidate WP_004127663.1 RHSP_RS29500 sugar ABC transporter permease
Query= TCDB::P29823 (298 letters) >NCBI__GCF_000359745.1:WP_004127663.1 Length = 286 Score = 224 bits (572), Expect = 1e-63 Identities = 117/284 (41%), Positives = 174/284 (61%), Gaps = 5/284 (1%) Query: 16 NGWLFVAPAIALISVFMLYPILRSLVLSLYTGRGMMLKFSGTGNLVRLWNDPVFWQALQN 75 + + F+AP + + + F ++PI+ S ++S R ++ + N RL+ DP F+ ALQN Sbjct: 7 SAYAFLAPYLLVFAAFWVWPIIDSFLISFQNTRVNPWVYNLSLNWGRLFGDPAFYNALQN 66 Query: 76 TVIFFVVQVPIMITMALILAAMLNNPKLRYSGLFRTMIFLPCVSSLVAYSILFKSMFSLD 135 T+I +VQVP+MIT+A ++A +LN+P L+ G+FR F P V VAY+ +F+ MF++D Sbjct: 67 TLIILIVQVPVMITLATVMAVLLNSPLLKARGIFRFAFFAPVVVGEVAYAAVFRLMFNVD 126 Query: 136 -GVVNNTLLAIGIIGEPIGWLTDPFWAKVLIIIAITWRWTGYNMIFYLAALQNIDRSIYE 194 G+VN L +G P+ W + A VLIIIA+TWRW GYN I L+ LQ+I +YE Sbjct: 127 FGIVNKLLGTVGFA--PVSWFAESHAAMVLIIIAVTWRWAGYNAIIILSGLQSIPEDVYE 184 Query: 195 AAKIDGVPSWGRFAFLTIPMLKPVILFTTITSTIGTLQLFDEVYNFTEGTGGPANSTLTL 254 AA +D V + +F +T+P+LKP+ILF + S IGT+QLF E Y T GGP T TL Sbjct: 185 AATLDRVNRFQQFIHITLPLLKPIILFCVVLSVIGTMQLFTEPYLIT-NRGGPGGGTETL 243 Query: 255 SLYIYNLTFRFMPSFSYAATVSYVIVLMVAVLSFLQFYAARERK 298 L +Y F+ +F YA+ V+Y + + +S L + RE K Sbjct: 244 GLLLYRQAFQ-STNFGYASAVAYTMAALAVAISLLNLWVGREPK 286 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: 290 Number of extensions: 19 Number of successful extensions: 4 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: 286 Length adjustment: 26 Effective length of query: 272 Effective length of database: 260 Effective search space: 70720 Effective search space used: 70720 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