GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Nocardioides daejeonensis MJ31

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_110205942.1 DNK54_RS05350 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU1
         (463 letters)



>NCBI__GCF_003194585.1:WP_110205942.1
          Length = 332

 Score =  138 bits (348), Expect = 2e-37
 Identities = 101/331 (30%), Positives = 160/331 (48%), Gaps = 40/331 (12%)

Query: 138 FGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGI 197
           FG   ++Y + A GLNI  G  GLL+ G  AF AVG Y+ A+  + + +S W+ + L+G+
Sbjct: 15  FGTSAIVYCLAAIGLNIHFGYTGLLNFGQAAFMAVGGYTMAMFVTQWDVSLWLAM-LAGL 73

Query: 198 -FAALWGVILGFPVLRLRGDYLAIVTLAFGEIIR-----LVLINWTDVTKGTFGISSIPK 251
              A+  ++LG P LRLR DYLAIVT+A  EI+R     + L  +     G    S+  +
Sbjct: 74  GLTAVLAILLGIPTLRLRADYLAIVTIAAAEIVRQVYGSIALKKYFGAQDGLTAFSADFR 133

Query: 252 A-TLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAW 310
           A   F  P D     + K       +  + + + + ++ALC L  ++   L R P GR  
Sbjct: 134 ALNPFDGPVDLGIVSWGK-------NDAWVVLVGWFVVALCCLVVWL---LMRSPWGRIL 183

Query: 311 EALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVIL 370
           +++REDE A RSLG N    K+ +   G M    AG   A +   ++P  F    +    
Sbjct: 184 KSIREDEDAVRSLGKNVYYYKMQSLMLGGMIGALAGFVTALKSAAINPSFFATDVTFFAY 243

Query: 371 AIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIF-------GPDFTP--------- 414
            ++++GG   + G  + AI+          ++FL L F       G    P         
Sbjct: 244 TVLLIGGAARVLGPVVGAII------FWFLLTFLDLFFSAATDDVGSVLIPSSIMTNQQA 297

Query: 415 ELYRMLIFGLAMVVVMLFKPRGFVGSREPTA 445
            L R ++ GLA++++M+F+P+G  G R   A
Sbjct: 298 SLVRFIVMGLALMLLMIFRPQGIFGDRRELA 328


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: 428
Number of extensions: 23
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: 332
Length adjustment: 31
Effective length of query: 432
Effective length of database: 301
Effective search space:   130032
Effective search space used:   130032
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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