Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_008031204.1 C0J26_RS03600 urea ABC transporter ATP-binding subunit UrtE
Query= uniprot:D8IUY7 (241 letters) >NCBI__GCF_003031005.1:WP_008031204.1 Length = 232 Score = 159 bits (403), Expect = 3e-44 Identities = 92/226 (40%), Positives = 140/226 (61%), Gaps = 8/226 (3%) Query: 5 ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64 +L+V +L YGG ++G+ +V GE+ L+G NG GKTT LK + G LPA EG + Sbjct: 1 MLQVDKLHQYYGGSHILRGLTFDVKVGEVTCLLGRNGVGKTTLLKCLMGLLPAK--EGAV 58 Query: 65 EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGA--YTSDDKGQIAADIDK 122 + G+P+ K + V +A VP+GR +F R++++ENLLMG + + ++ A I + Sbjct: 59 NWEGKPITTFKPHQRVHAGIAYVPQGREIFGRLTVEENLLMGLSRFPGSEAKEVPAFIYE 118 Query: 123 WFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEV 182 F V ++K+R G LSGG+QQ LA+ RAL S P+LL+LDEP+ G+ P ++++I V Sbjct: 119 LFPVLLQMKQRRG---GDLSGGQQQQLAIGRALASRPRLLILDEPTEGIQPSVIKEIGAV 175 Query: 183 IRNVSAQG-ITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQM 227 I+ ++A+G + ILLVEQ A E A + VM G I QG+ + M Sbjct: 176 IKKLAARGDMAILLVEQFYDFAAELADQYLVMSRGEIVQQGRGENM 221 Lambda K H 0.317 0.134 0.365 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: 163 Number of extensions: 13 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: 241 Length of database: 232 Length adjustment: 23 Effective length of query: 218 Effective length of database: 209 Effective search space: 45562 Effective search space used: 45562 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 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