Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_011767166.1 AZO_RS17300 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000061505.1:WP_011767166.1 Length = 355 Score = 139 bits (349), Expect = 1e-37 Identities = 107/346 (30%), Positives = 171/346 (49%), Gaps = 46/346 (13%) Query: 10 IGAVALLV-----LPLILQSFGNAWVR-IADLALLYVLLALGLNIVVGYAGLLDLGYVAF 63 IG A+LV +PL+ + W++ I L++ L A+GLNI+ GYAG L LG AF Sbjct: 27 IGFAAILVFFFGVVPLVANQY---WLQAILIPVLIFSLAAIGLNILTGYAGQLSLGSAAF 83 Query: 64 YAVGAYLFALMASPHLADNFAAFAAMFP-NGLHTSLWIVIPVAALLAAFFGAMLGAPTLK 122 AVGA F A+ M +G+ + IV+ L AA G G P+L+ Sbjct: 84 MAVGA--------------FGAYNFMLRIDGMPFLVGIVL--GGLCAAAVGVAFGLPSLR 127 Query: 123 LRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFD 182 ++G YLA+ TL I L N + G+ +R+E+ G+ Sbjct: 128 IKGFYLAVATLAAQFFIVWALVKFPWFSNHASS-------------GVITAQRVEILGYA 174 Query: 183 INSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFG 242 +S Y L L +V V ++ L S GR+WMA+R+ ++AA+ +GI + KL AF Sbjct: 175 FDSPVSKYLLTLAVVAVLALLAKNLVRSTTGRSWMAVRDMDVAAEVIGIRPMHAKLTAFA 234 Query: 243 MGASFGGVSGAMFG-AFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALP 301 + + + GV+GA++ + G V PE FSL S I+ M+++GG+G I G GA + +P Sbjct: 235 VSSFYCGVAGALYAYTYLGTVEPEGFSLDLSFKILFMIIIGGVGSIMGSFFGAAFIVLMP 294 Query: 302 EVLRYVAGPLQAMTDGRLDSAI---LRQLLIALAMIIIMLLRPRGL 344 L V + ++ G + + + L ++ +I +++ P GL Sbjct: 295 IFLNVV---MHSVFGGAMPAGMGSNLELIIFGGLIIFFLIVEPHGL 337 Score = 29.6 bits (65), Expect = 1e-04 Identities = 37/166 (22%), Positives = 66/166 (39%), Gaps = 35/166 (21%) Query: 9 IIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFY---- 64 ++ +ALL L+ + G +W+ + D+ + A + I +A L +FY Sbjct: 188 VVAVLALLAKNLVRSTTGRSWMAVRDMD----VAAEVIGIRPMHAKLTAFAVSSFYCGVA 243 Query: 65 -AVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKL 123 A+ AY + P +F +F + I+ V +++ +FFGA Sbjct: 244 GALYAYTYLGTVEPEGFSLDLSFKILF-------MIIIGGVGSIMGSFFGA--------- 287 Query: 124 RGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFG 169 F ++ IFLN + H V P G+G + +FG Sbjct: 288 ----------AFIVLMPIFLNVVMHSVFGGAMPAGMGSNLELIIFG 323 Lambda K H 0.328 0.144 0.430 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: 350 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 358 Length of database: 355 Length adjustment: 29 Effective length of query: 329 Effective length of database: 326 Effective search space: 107254 Effective search space used: 107254 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: 49 (23.5 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