Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF1247 PGA1_c12630 putative high-affinity branched-chain amino acid transport ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__Phaeo:GFF1247 Length = 251 Score = 171 bits (433), Expect = 1e-47 Identities = 98/238 (41%), Positives = 143/238 (60%), Gaps = 6/238 (2%) Query: 7 TGQPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTIC--GSPQAR 64 T L V + YYG + G+ +V++GEI++L+G NGAGK++ + +I GSP Sbjct: 16 TAPAFLSVWDMHAYYGESYIVQGISFNVHEGEILALLGRNGAGKTSTLRSIARTGSPMVT 75 Query: 65 TGSVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVE 124 G + + + + +M +HE + + PE RRI P +TV ENLQ+ + +E Sbjct: 76 KGEIWLDHQPLHKMSSHEASAAGLGLVPEDRRIIPGLTVEENLQLAQIAPPV---GWSIE 132 Query: 125 KIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFE 184 +++ LFPRL ER Q G TLSGGEQQML+I RAL K+LLLDEP GLAP+IV I + Sbjct: 133 RLYELFPRLGERRKQEGVTLSGGEQQMLAIARALARDIKVLLLDEPYEGLAPVIVDEIEK 192 Query: 185 AIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 + + + +G+T +VEQNA AL L+ RA ++ G + G+ E+L N E+RA YL Sbjct: 193 TLIHIKQ-QGITTVIVEQNAVRALELADRAVILDTGGIVFDGAAAEVLENEELRAEYL 249 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: 187 Number of extensions: 11 Number of successful extensions: 4 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: 251 Length adjustment: 24 Effective length of query: 223 Effective length of database: 227 Effective search space: 50621 Effective search space used: 50621 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: 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