Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate WP_015930502.1 MNOD_RS18710 branched-chain amino acid ABC transporter permease
Query= SwissProt::P22729 (425 letters) >NCBI__GCF_000022085.1:WP_015930502.1 Length = 295 Score = 144 bits (364), Expect = 3e-39 Identities = 101/308 (32%), Positives = 161/308 (52%), Gaps = 37/308 (12%) Query: 112 VDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYTFALLNHYYGLGFWTCLPIA 171 + I ++ IY++L LGLN+ GL+G+ G+ GF+ IGAYT ALL+ W +A Sbjct: 6 IAILIISGIYVLLALGLNLQYGLTGITNFGHVGFFCIGAYTAALLSQVSVP--WPFAFLA 63 Query: 172 GL-MAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNNTEITGGPNGISQIPKPTL 230 G +AA + LG L+LR DY AIV+LGF E+VRI++ + +T G GI+ IPK L Sbjct: 64 GAALAALTAWPLGLISLKLRDDYFAIVSLGFSEVVRIVVTSEKWLTKGVQGITGIPK--L 121 Query: 231 FGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVALLLVVLSLFVINRLLRMPLGRA 290 F F G + V+ L + +L LS +R++R P GR Sbjct: 122 FA-----------------FLGTGITQAVAVLLLLVAVNVLAGLSK---SRIVRSPFGRM 161 Query: 291 WEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGTLFAARQGFVSPESFTFAESAFV 350 EA+R++E A ++LG P + K+ + AA AG AG +A G++ PE F + ++ Sbjct: 162 IEAIRDNEEAVKALGKDPSKFKIQVLMLGAALAGIAGGFYAHYIGYIVPEQFVPLITFYI 221 Query: 351 LAIVVLGGMGSQFAVILAAILLV-------VSRELMRDFNEYSML-----MLGGLMVLMM 398 +++GG+G ++ ++L+ R L+ +E M ++G +VL Sbjct: 222 WMAIIIGGVGPISGALVGTLILMFFLEGSRFLRGLIPFVSEVEMASIRLGVIGLALVLFT 281 Query: 399 IWRPQGLL 406 ++RPQGL+ Sbjct: 282 LYRPQGLM 289 Lambda K H 0.330 0.145 0.436 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: 253 Number of extensions: 9 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: 425 Length of database: 295 Length adjustment: 29 Effective length of query: 396 Effective length of database: 266 Effective search space: 105336 Effective search space used: 105336 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: 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