Align GtsC (GLcG), component of Glucose porter, GtsABCD (characterized)
to candidate WP_017616633.1 CDO52_RS13840 carbohydrate ABC transporter permease
Query= TCDB::Q88P36 (281 letters) >NCBI__GCF_002263495.1:WP_017616633.1 Length = 315 Score = 155 bits (393), Expect = 8e-43 Identities = 96/273 (35%), Positives = 157/273 (57%), Gaps = 13/273 (4%) Query: 16 AIHAVLLIAVLLYLVPLVVMLLTSFKTPEDITTGN---LLSWPAVIT---GIGWVKAWGA 69 AI +L++ L +L+P + + ++S ++P+D + +L+ P+ +T G + G Sbjct: 48 AIQVLLVLVGLFWLLPTLGLFVSSLRSPQDNASSGWWTVLAAPSRLTLENYAGLLDNEGF 107 Query: 70 VSGYFWNSIMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPA 129 V+ +F N+I+I+VP+ ++ I AL Y + F G F ++ +P Q L+P Sbjct: 108 VASFF-NTILISVPSTVLIVVIAALAAYAFAWMEFPGRDWLFLGVVGLLVVPLQVALIPI 166 Query: 130 SFTLGKLGLASTTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKAARLDGAGFFTIFRR 189 + G LG+ + G+VL HV +GL F RNF+ +IP L++AAR+DG TIFRR Sbjct: 167 AQVYGPLGIYGSIPGVVLFHVGFGLPFAIFLLRNFFAAIPRDLLEAARMDGGKELTIFRR 226 Query: 190 IILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVNTSTGAKEYNVDM 249 +ILP+ P I I+QF +WND L +VF+ +QP+TVAL + + GA N+D+ Sbjct: 227 VILPLGGPAIASLAIFQFLWVWNDLLVALVFADSANQPMTVALQSEMR-QFGA---NIDV 282 Query: 250 --AAAMIAGLPTLLVYVVAGKYFVRGLTAGAVK 280 + A ++ + LLV+ +YFV+G+ AGAVK Sbjct: 283 ISSGAFLSMVVPLLVFFAFQRYFVQGVMAGAVK 315 Lambda K H 0.329 0.142 0.443 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: 226 Number of extensions: 9 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: 281 Length of database: 315 Length adjustment: 26 Effective length of query: 255 Effective length of database: 289 Effective search space: 73695 Effective search space used: 73695 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