Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_023434295.1 N177_RS20200 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000496075.1:WP_023434295.1 Length = 441 Score = 430 bits (1105), Expect = e-125 Identities = 238/458 (51%), Positives = 302/458 (65%), Gaps = 29/458 (6%) Query: 10 KPDAGLVRKGLTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFVAVAAIG 69 +P A LV+ +A ++A+++ + +GL+T L + RW + + V G Sbjct: 9 RPAAELVK----DAAYSALIALALAAPIIGLQT-VTARGGLGLNARWDDVFLIVLAVFAG 63 Query: 70 RFAMVVFIRPNIDRRKLSKA---REGELDISTEKSFFHRHFLKIALIALLLYPMVVVAIK 126 R + I + R + + R G + + +AL LL P + + + Sbjct: 64 RLLLNFTIWRHQGARPIGQKWFQRAGGRPFARHGHTLSKIIGPLALAVALLLPALPFSDR 123 Query: 127 GPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGL 186 YV + I +L Y+ML WGLNIVVGLAGLLDLGYVAFYA+GAYS+ALL+++F L Sbjct: 124 -------YVMDLSIMVLTYIMLGWGLNIVVGLAGLLDLGYVAFYAIGAYSFALLATHFDL 176 Query: 187 SFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGI 246 FW+ LPL+GI AA WGVILGFPVLRLRGDYLAIVTLAFGEIIR+VL+NW + T G GI Sbjct: 177 GFWICLPLAGILAAFWGVILGFPVLRLRGDYLAIVTLAFGEIIRVVLLNWYEFTGGPNGI 236 Query: 247 SSIPKATLFGIPFDATAGG-FAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMP 305 IP TLFG+ F F + F L SS + IFL+Y+IL L ++T +VT+RLRR+P Sbjct: 237 LGIPDPTLFGLEFARRGDNTFHEFFGLSYSSMHKIIFLYYIILCLALITNFVTLRLRRLP 296 Query: 306 IGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLE 365 +GRAWEALREDEIACRSLGINT TKLTAFA GAMF GFAGSFFA RQGF+SPESF F+E Sbjct: 297 VGRAWEALREDEIACRSLGINTTNTKLTAFAIGAMFGGFAGSFFATRQGFISPESFTFIE 356 Query: 366 SAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLA 425 SA+ILAIVVLGG+GS G+ IAAIVM+GG E RE E YRMLIFGLA Sbjct: 357 SALILAIVVLGGLGSQVGVVIAAIVMMGGFEYFREF-------------EQYRMLIFGLA 403 Query: 426 MVVVMLFKPRGFVGSREPTAFLRERKAISGSFIKEGHG 463 MV +M+++PRG + +R P+ L+ERKAI + +GHG Sbjct: 404 MVFIMVWRPRGLISTRSPSVILKERKAIGADLVGQGHG 441 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: 673 Number of extensions: 36 Number of successful extensions: 3 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: 463 Length of database: 441 Length adjustment: 33 Effective length of query: 430 Effective length of database: 408 Effective search space: 175440 Effective search space used: 175440 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