Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_029133949.1 A3GO_RS0114170 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000428045.1:WP_029133949.1 Length = 410 Score = 319 bits (817), Expect = 1e-91 Identities = 184/406 (45%), Positives = 255/406 (62%), Gaps = 34/406 (8%) Query: 49 ELIIVQRWGLLAIFVAVAAIGRFAMVVFIRP-NIDRRK-LSKAREGELDISTEKSFFHRH 106 E I+ RW + FVA IG F + + IR N + K L + + D +T + Sbjct: 33 ERTIIWRWENM-FFVA---IGSFVLSILIRVVNTQKTKRLERRSASDSDTTTSEPLIQVI 88 Query: 107 FLKIALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGY 166 + L + V A+ P TY N L+YV+L GLNIVVG+AGLLDLG+ Sbjct: 89 LQNPRYLYPLAGAVTVFALVFPYLFDTYQTNIMTTALMYVVLGLGLNIVVGMAGLLDLGF 148 Query: 167 VAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFG 226 VAFYAVGAYSYALL+++FG+ FW+ LP+ +FAA +G+ILGFPVLRLRGDYLAIVTL FG Sbjct: 149 VAFYAVGAYSYALLNAHFGIGFWMALPIGALFAASFGIILGFPVLRLRGDYLAIVTLGFG 208 Query: 227 EIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYL 286 EIIRL+L NW + ++G GIS+IP+ +FGI A ++++Y+ Sbjct: 209 EIIRLILENWNEFSQGPSGISNIPRPGMFGIELSLEAA---------------ILYIYYI 253 Query: 287 ILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAG 346 ++AL ++T +V RL+ +GRAW ALREDEIAC+++GI+ TKLTAFA GA +AG G Sbjct: 254 MVALVIVTIFVVNRLQDSRLGRAWIALREDEIACQAMGIDKTKTKLTAFALGATWAGMMG 313 Query: 347 SFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKL 406 FAA+ F++P SF FLESA+IL+IVVLGGMGS+ G+ + A+V++ E LR +S Sbjct: 314 VIFAAKTTFINPASFTFLESAIILSIVVLGGMGSILGVIVGALVLILLPEYLRALSD--- 370 Query: 407 IFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVGSREPTAFLRERKA 452 YRML FG +VV+M+FKP+G + + T +++K+ Sbjct: 371 ----------YRMLAFGAILVVMMIFKPQGIISNVRRTYKYQKQKS 406 Lambda K H 0.330 0.145 0.432 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: 562 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 463 Length of database: 410 Length adjustment: 32 Effective length of query: 431 Effective length of database: 378 Effective search space: 162918 Effective search space used: 162918 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 (21.8 bits) S2: 51 (24.3 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