Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate Ac3H11_1956 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
Query= reanno::pseudo5_N2C3_1:AO356_00470 (220 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1956 Length = 252 Score = 107 bits (268), Expect = 2e-28 Identities = 71/204 (34%), Positives = 104/204 (50%), Gaps = 16/204 (7%) Query: 25 SVQCSLLAIVLGTLIGLVAGL-----VLTYGRTWMRAPFRFYVDLIRGTPVFVLVLACFY 79 S+ +LA+VLG+LIG + L ++ G W V+L R P+ V + ++ Sbjct: 45 SLLALVLALVLGSLIGTLRTLQDRPMIVRLGNAW--------VELFRNIPLLVQIFLWYH 96 Query: 80 MAPALG---WQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQAIGLTFYQSL 136 + P+L + F VL L F + +AE VR +QALPRGQ A A+G T +Q+ Sbjct: 97 VIPSLFPVMKGVPGFALVVLALGFFTSARIAEQVRSGIQALPRGQRYAGMAVGFTTFQTY 156 Query: 137 GYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFAG 196 YVLLP A R I+P + + I K S++ + VAEL + Q T +E YL Sbjct: 157 RYVLLPMAFRIIIPPLTSETMNIFKNSSVAFAVSVAELTMFAMQAQEETSRGIEVYLAVT 216 Query: 197 FLFFIINYAIELLGRHIEKRVALP 220 L+ I +AI + IEKRV +P Sbjct: 217 SLYIISAFAINRIMAFIEKRVRIP 240 Lambda K H 0.330 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: 165 Number of extensions: 8 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: 220 Length of database: 252 Length adjustment: 23 Effective length of query: 197 Effective length of database: 229 Effective search space: 45113 Effective search space used: 45113 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: 46 (22.3 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