Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_053543734.1 CDES_RS00135 sugar ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >NCBI__GCF_001277995.1:WP_053543734.1 Length = 253 Score = 241 bits (616), Expect = 8e-69 Identities = 126/251 (50%), Positives = 171/251 (68%), Gaps = 3/251 (1%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66 LI+++ + K +G+ AL +++ V GE C+LGDNGAGKST IK +SG+H T G+++ Sbjct: 4 LIQLKDVSKKYGAFQALKDINISVRAGEVTCVLGDNGAGKSTLIKILSGLHPTTSGEVIV 63 Query: 67 EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126 G+ ++F+ PRDA+ AGIATV+Q LA++ MSV RNFF+G E + G +K D R Sbjct: 64 AGETVNFSSPRDALDAGIATVYQDLAVVGQMSVWRNFFLGQELTGRFGTMKKED---MRR 120 Query: 127 ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTAN 186 IT E++R+MGI LR D V +LSGG+RQ VAIARA++FGA+VLILDEPT+ALGV+Q+ Sbjct: 121 ITDEQLREMGIELRNVDVPVASLSGGQRQVVAIARAIYFGARVLILDEPTAALGVKQSGM 180 Query: 187 VLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 VL I R +G+ V+FITHN HA VGD F +LN G+ R ++ EEL M+G Sbjct: 181 VLRFISAARDRGIGVIFITHNPHHAYLVGDHFILLNLGQQAMDKSRSEVELEELTLAMSG 240 Query: 247 GQELATLEGSL 257 G EL TL L Sbjct: 241 GGELDTLSHEL 251 Lambda K H 0.321 0.137 0.395 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: 212 Number of extensions: 7 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: 261 Length of database: 253 Length adjustment: 24 Effective length of query: 237 Effective length of database: 229 Effective search space: 54273 Effective search space used: 54273 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 (21.9 bits) S2: 47 (22.7 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