Align ABC transporter permease (characterized, see rationale)
to candidate WP_013418504.1 RVAN_RS04120 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000166055.1:WP_013418504.1 Length = 304 Score = 263 bits (671), Expect = 5e-75 Identities = 148/307 (48%), Positives = 198/307 (64%), Gaps = 15/307 (4%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSW-SCIGMMQG 59 MD QQ+INGL LGS+Y LIA+GYTMVYGI+ +INFAHGEV MIGA + + + + Sbjct: 1 MDYFAQQLINGLTLGSIYGLIAIGYTMVYGIVGMINFAHGEVFMIGAFIALIAVLSLFAL 60 Query: 60 AMPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLA 119 + P + LLLA +IA + + IE++AYRPLR+S RLAPLITAIGMSI LQT Sbjct: 61 GVTAVP--LALLLALVIAMALTGLWGWAIERLAYRPLRNSFRLAPLITAIGMSIALQTFV 118 Query: 120 MIIWKPNYKPYPTMLPSS-PFEIGGAF---ITPTQILILGVTAVALASLVYLVNHTNLGR 175 + KP P ++ G F ++ QILI+ T V +A+ YL+N T+LGR Sbjct: 119 ALTQGARSKPLPPVIRGGFTLSEGNGFAVSLSYMQILIIVTTVVVMAAFSYLINSTSLGR 178 Query: 176 AMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKA 235 A RA ++ ++A+L GV D IS TF+IGA LAA+AG+M+ + YG +GF+ G+KA Sbjct: 179 AQRACEQDRKMAALCGVNVDRTISLTFVIGAALAAVAGLMFLAYYGVIDFFVGFVAGIKA 238 Query: 236 FTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTL 295 FTAAV GGIG+L GA++GG+L+GLIE +GY + Y D+ AF +L I+L Sbjct: 239 FTAAVLGGIGSLPGAMLGGLLIGLIEVFWAGY--------FTAQYKDVAAFSILAIVLIF 290 Query: 296 RPSGLLG 302 PSGLLG Sbjct: 291 MPSGLLG 297 Lambda K H 0.327 0.142 0.419 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: 254 Number of extensions: 11 Number of successful extensions: 5 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: 309 Length of database: 304 Length adjustment: 27 Effective length of query: 282 Effective length of database: 277 Effective search space: 78114 Effective search space used: 78114 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: 48 (23.1 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