Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_013451938.1 CALNI_RS09200 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000183405.1:WP_013451938.1 Length = 350 Score = 157 bits (398), Expect = 4e-43 Identities = 103/336 (30%), Positives = 171/336 (50%), Gaps = 33/336 (9%) Query: 109 KIALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVA 168 K A + +Y +++ P + +Y+ I I + A GLNI+ G GL+ LG+ A Sbjct: 21 KTAFSKISVYSFLILMFLVPFHANSYILYILNMIFISSIAAVGLNILTGFTGLISLGHGA 80 Query: 169 FYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEI 228 F VGA++ L+ +G++F+ +PL+ +F A+ G+I G P LRL+ YL+I TLA I Sbjct: 81 FIGVGAFATGYLAMNYGMNFYFAIPLAALFTAIIGIIFGLPSLRLKDLYLSIATLAAQFI 140 Query: 229 IRLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLIL 288 + + I T G G+ + T+FGI + ++ + F Sbjct: 141 LEFIFIRAESFTGGVNGM-PVASPTIFGIEINND----------------FRFYFFAYSF 183 Query: 289 ALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSF 348 A+ M+T V + R IGRA+ ++R++ IA ++G++ KL +F + +AG AGS Sbjct: 184 AIIMIT--VAKNILRTRIGRAFISVRDNYIAAEAMGVDVFKYKLLSFGISSFYAGIAGSL 241 Query: 349 FAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREM------- 401 +A F++PE F S L+++++GG+GSL G I +V E+LR + Sbjct: 242 WAYYVQFITPEHFTITVSIQYLSMIIIGGLGSLLGSIFGTIFIVILPEILRHIVDLLSGA 301 Query: 402 -SFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRG 436 FLK IF R +GL +++ +LF+P G Sbjct: 302 APFLKQIF------PAIREAFYGLVIILFLLFEPEG 331 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: 530 Number of extensions: 42 Number of successful extensions: 4 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: 350 Length adjustment: 31 Effective length of query: 432 Effective length of database: 319 Effective search space: 137808 Effective search space used: 137808 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