Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_011842475.1 RSPH17029_RS18135 amino acid ABC transporter permease
Query= TCDB::Q52665 (434 letters) >NCBI__GCF_000015985.1:WP_011842475.1 Length = 370 Score = 216 bits (551), Expect = 7e-61 Identities = 141/428 (32%), Positives = 213/428 (49%), Gaps = 70/428 (16%) Query: 4 TSFVRTEMLAPRPA---PVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAAAPW- 59 +S + + AP A P +++ A W+R NLFS + LT+ + + W Sbjct: 2 SSVPSSPLAAPAAAAYDPDARLSAPAWLRANLFSSVWQSLLTLVVAVVLIRFFWFVLDWG 61 Query: 60 LLHGVWNANSLTECRAIIAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFVTFAG 119 +++ V+ CRA ATGACWAVI + LFG YP D++WRL + A Sbjct: 62 VVNAVFYTTDPDVCRA---------ATGACWAVIVEKHRPMLFGLYPYDEHWRLVLMMA- 111 Query: 120 LFLALAPVLFDALPRKLIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTALAPK 179 + L V+ PR W L + P+W S+ G + G Sbjct: 112 --VYLGTVVLSLWPR--CWN----------LRFLVPLWIVSSLSIGILMFG--------- 148 Query: 180 LGVPVSAGIGLVVAALFWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIGVTAIV 239 GV L L V + ++GG L +++ ++ Sbjct: 149 -GV-------------------------------LGLRYVPTSEWGGLPLTMLLFTGTVL 176 Query: 240 VSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGTNFDLI 299 + +P+ +LLALGR++ + + + +SV IE +RGVPLIT+LF A + FLP G + + Sbjct: 177 IGMPVAVLLALGRRAPLPVARGVSVVFIEALRGVPLITILFVAVNVFPLFLPAGVEVNKL 236 Query: 300 LRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPG 359 LR+ + + +F A Y AEVIRGGL A+P GQYEAA +L L YWQ R II+PQAL+IS+P Sbjct: 237 LRITVGIAIFFACYQAEVIRGGLQAIPTGQYEAAASLSLSYWQTTRRIILPQALRISLPA 296 Query: 360 IVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMS 419 I + I K+T+ V +GLFD L + V D W+ Y E Y+FVA ++ F +++S Sbjct: 297 ITNHIIAAMKNTSFVIIIGLFDILTA-TTAVMQDPLWRKFYIEAYLFVAAVYLFFGYALS 355 Query: 420 RYSMYLER 427 Y+ +E+ Sbjct: 356 LYARQVEK 363 Lambda K H 0.329 0.143 0.457 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: 568 Number of extensions: 39 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 434 Length of database: 370 Length adjustment: 31 Effective length of query: 403 Effective length of database: 339 Effective search space: 136617 Effective search space used: 136617 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. 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