Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_011767541.1 AZO_RS19165 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000061505.1:WP_011767541.1 Length = 315 Score = 139 bits (351), Expect = 8e-38 Identities = 103/312 (33%), Positives = 153/312 (49%), Gaps = 35/312 (11%) Query: 33 ADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAAMFPN 92 A L + Y + LGL IVVG+ G + LG+ A A+GAY AL+ + L A Sbjct: 35 ATLVITYAIAGLGLVIVVGHGGQIALGHGALVALGAYTQALLVARGLPPLLA-------- 86 Query: 93 GLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNL 152 +P+A GA+ P +L G Y I TL F ++ L + +L Sbjct: 87 ---------LPLAMAAGGAGGALASLPARRLGGLYFGISTLAFALLVEEALVRWE---SL 134 Query: 153 TNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRI 212 T G GLG V F V G+ + + VL+ ++ C RL SRI Sbjct: 135 TRGSAGLG----VAAFS--------VGGWSATAPAAQLGVSAVLLALAWAGCRRLLASRI 182 Query: 213 GRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMES 272 GRAW A+REDE+AA+A GI LAF G + G+ GA++ + G++SPE F L S Sbjct: 183 GRAWRALREDEMAAQACGIAAGPSIALAFTAGGALAGLGGALYAHWIGYLSPEQFGLRFS 242 Query: 273 VMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALA 332 ++ +V +GG + G + GA+++ ALP++ +A A+ L SA + LL Sbjct: 243 FELLMLVFIGGARRLAGALWGALVIVALPQL---IALARDALPGDTLRSAGVETLLFGAL 299 Query: 333 MIIIMLLRPRGL 344 ++ +LLRP+GL Sbjct: 300 IVAAVLLRPQGL 311 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: 300 Number of extensions: 16 Number of successful extensions: 2 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: 358 Length of database: 315 Length adjustment: 28 Effective length of query: 330 Effective length of database: 287 Effective search space: 94710 Effective search space used: 94710 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