Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate AZOBR_RS15675 AZOBR_RS15675 ABC transporter permease
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__azobra:AZOBR_RS15675 Length = 224 Score = 87.0 bits (214), Expect = 4e-22 Identities = 65/195 (33%), Positives = 99/195 (50%), Gaps = 10/195 (5%) Query: 179 WLVVILAIA-----LVLFVSWLAQRQRSPRDWRWLYGA-IAVVTVLMLLTQLSWPQQLQP 232 WL V L+I L++ + + P+ RW+ A I VV L Q+ + Sbjct: 22 WLTVQLSIGAMVLGLIVAILCALGKTSGPKPVRWVINAYIEVVRNTPFLVQIFL---IFF 78 Query: 233 GQIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQ 292 G G+RLS + AL+ +V GA+ TEIIR GI S+ GQ EA ALGL Q Sbjct: 79 GLPTMGVRLSPDLAALI-AMVVNVGAYATEIIRAGIESIQKGQIEAGLALGLKPLQVFRY 137 Query: 293 IVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLT 352 IV+ ALR + P+L SQ++ +SS+ A+ +L + A +QT R E+++++ Sbjct: 138 IVIKPALRTVYPALTSQFILLMLSSSVVSAISADELTSVANNIQSQTFRSFEIYIVVTGI 197 Query: 353 YLAINAVISAGMNGL 367 YL + + SA G+ Sbjct: 198 YLMLAMMFSALFAGI 212 Score = 31.6 bits (70), Expect = 2e-05 Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%) Query: 93 IAIG-LILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVWYF 143 ++IG ++L ++ L + S +R + Y+ VVRNTP L+Q+ + +F Sbjct: 27 LSIGAMVLGLIVAILCALGKTSGPKPVRWVINAYIEVVRNTPFLVQIFLIFF 78 Lambda K H 0.326 0.140 0.445 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: 188 Number of extensions: 11 Number of successful extensions: 2 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: 377 Length of database: 224 Length adjustment: 26 Effective length of query: 351 Effective length of database: 198 Effective search space: 69498 Effective search space used: 69498 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 (21.7 bits) S2: 48 (23.1 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