Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_089303489.1 CHB84_RS21580 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_900188115.1:WP_089303489.1 Length = 330 Score = 142 bits (359), Expect = 1e-38 Identities = 101/306 (33%), Positives = 150/306 (49%), Gaps = 14/306 (4%) Query: 145 YVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGV 204 YV+ A GLNI G GLL+ G VAF VGAY A+ S FGLS WV + + + AA+ + Sbjct: 22 YVLAAIGLNIHFGYTGLLNFGQVAFMLVGAYGVAISVSTFGLSMWVGVLVGILAAAVLAL 81 Query: 205 ILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWT--DVTKGTFGISSIPKATLFGIPFDAT 262 ILG P LRLR DYLAI T+A GE++RL + +T G +G+ L + Sbjct: 82 ILGIPALRLRSDYLAISTIAAGEVLRLFYRSSVAEPLTGGVYGLQRFGDDLL---DLNPV 138 Query: 263 AGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRS 322 G ++ P++ ++L + L L + L P GR A+REDE A RS Sbjct: 139 PPGIYEVG--PLAFTARDVWLMSVGWGLVALVVILVYLLIHSPWGRVIRAIREDEEAARS 196 Query: 323 LGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLT 382 LG N KL + G + G F Q P+ F + + + ++VLGG G + Sbjct: 197 LGKNVYAYKLQSLVLGGVIGALGGMVFTIHQQSAHPDGFDPVVTFFLYTMLVLGGAGRVF 256 Query: 383 GIAIAAI----VMVGGTELLREMSFLKLIFGPDFTPE---LYRMLIFGLAMVVVMLFKPR 435 G + + +M+ LRE+ I P R+ + GL ++++M F+P+ Sbjct: 257 GPVLGGLLFWFLMLSFDAFLRELMATGYIPPEILVPSDVGALRLALVGLGLLLLMAFRPQ 316 Query: 436 GFVGSR 441 G +G+R Sbjct: 317 GILGNR 322 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: 507 Number of extensions: 35 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: 330 Length adjustment: 31 Effective length of query: 432 Effective length of database: 299 Effective search space: 129168 Effective search space used: 129168 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: 50 (23.9 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