Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 5210162 Shew_2606 ABC transporter-related protein (RefSeq)
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__PV4:5210162 Length = 272 Score = 205 bits (522), Expect = 7e-58 Identities = 113/242 (46%), Positives = 156/242 (64%), Gaps = 7/242 (2%) Query: 10 PLLQVNGVETYYGN-IRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICG-----SPQA 63 PLL +N +E Y + I+ L GV + V +GEIV+L+G NGAGKST + I G + + Sbjct: 12 PLLAINNIEVVYDDVIQVLRGVSIEVPQGEIVTLLGPNGAGKSTTLKAISGLLKTENGEV 71 Query: 64 RTGSVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDV 123 G + F G I ++ R + Q EGRRI MTV+ENL++GA +D+ Sbjct: 72 SRGDIHFMGERIDVKNADDVVRSGLFQVMEGRRIVEDMTVIENLKLGAYTRRDGQVNQDI 131 Query: 124 EKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIF 183 E +F FPRLKER G LSGGEQQML+IGRALMARPK++ LDEPS+GL+PL+VK +F Sbjct: 132 EMVFNYFPRLKERTGL-AGYLSGGEQQMLAIGRALMARPKMICLDEPSMGLSPLLVKEVF 190 Query: 184 EAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLE 243 I K+N +G+T+ LVEQNA AL+ ++ Y+M +GK+ + G+ +LL N +V+ YL Sbjct: 191 GIIEKINREQGITMLLVEQNANYALKAANYGYIMESGKIVLDGTKAQLLNNEDVKEFYLG 250 Query: 244 GG 245 GG Sbjct: 251 GG 252 Lambda K H 0.320 0.137 0.387 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: 213 Number of extensions: 10 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: 247 Length of database: 272 Length adjustment: 24 Effective length of query: 223 Effective length of database: 248 Effective search space: 55304 Effective search space used: 55304 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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