GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natC in Herbaspirillum autotrophicum IAM 14942

Align NatC, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_050462656.1 AKL27_RS09910 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= TCDB::Q8YY08
         (377 letters)



>NCBI__GCF_001189915.1:WP_050462656.1
          Length = 408

 Score =  147 bits (371), Expect = 5e-40
 Identities = 108/354 (30%), Positives = 174/354 (49%), Gaps = 69/354 (19%)

Query: 15  FALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLSLK-GVPLFISAIVGAIFAALLGL 73
           + +  LGLN+  GF GL++ G++ F  +G YT  LL+   G+  +    + A  +AL G 
Sbjct: 112 YVVLGLGLNIVVGFAGLLDLGYVGFYAVGGYTYALLNQYFGLSFWECLPLAAGMSALFGF 171

Query: 74  VIGFATLRLREDYLAIVTIGTGELIRLVVNNQDLPVGDTWVSGAFGVQSYPIPLSTEPNL 133
           ++GF  LRLR DYLAIVT+G GE+IRL++NN     G     G  GV   P P       
Sbjct: 172 LLGFPVLRLRGDYLAIVTLGFGEIIRLLLNNLTSLTG-----GPDGVSGIPKP------- 219

Query: 134 FFRLLMIGILTLLFAVTVFSLWRWIRNAQKLQLTDATDKTSSKQEIASRFGVGIILGLLA 193
                           TVF +        ++  T + +  ++  ++         LGL  
Sbjct: 220 ----------------TVFGI--------EMARTASVEGGTTFHDM---------LGLT- 245

Query: 194 TAIYISGVITLYNYIPKAGLMLVSLLVLAFVFWRLEYLVRSPWGRVLKAIREDEEIPKAM 253
              Y  G + ++ Y        + LL++ F ++    L+R P GR  +A+R+DE   +++
Sbjct: 246 ---YQGGHMVIFLYF-------LGLLLVLFTYFVTSRLIRMPMGRAWEALRDDEIACRSL 295

Query: 254 GKNVFWYKLQSLMLGGAIAGIAGAFFAWQISAIYPDNFQPQLTFDSWIMVILGGAGNNIG 313
           G N    KL +  LG A AG+AG+FFA +   + P++F    +     +V+LGG G+ +G
Sbjct: 296 GINPTKIKLSAFTLGAAFAGLAGSFFAARQGLVNPESFTFIESALILAIVVLGGMGSQLG 355

Query: 314 SILGAVIYFAYDAITREVLPKIIPLDEARLGAFRIMCIGLILMVLMIWRPQGIL 367
            IL A            +L  I+P        +R++  GL+++++MIWRPQG+L
Sbjct: 356 VILAA------------ILLTILPEVARSFAEYRMLIFGLVMVLMMIWRPQGLL 397


Lambda     K      H
   0.328    0.145    0.441 

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: 455
Number of extensions: 24
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 377
Length of database: 408
Length adjustment: 31
Effective length of query: 346
Effective length of database: 377
Effective search space:   130442
Effective search space used:   130442
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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