GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natC in Magnetospirillum magneticum AMB-1

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_011384209.1 AMB_RS09130 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= TCDB::Q8YY08
         (377 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384209.1 AMB_RS09130 high-affinity
           branched-chain amino acid ABC transporter permease LivM
          Length = 415

 Score =  126 bits (317), Expect = 1e-33
 Identities = 104/369 (28%), Positives = 167/369 (45%), Gaps = 72/369 (19%)

Query: 5   LIFLAISTATFALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLSLK-GVPLFISAIV 63
           L+  A     + +   GLN+  G  GL++ G +AF  +GAY+  LLS   G+  ++   +
Sbjct: 108 LVDKATLVLIYVMLGWGLNIVVGLAGLLDLGFVAFYAVGAYSYALLSQTFGLSFWVCLPL 167

Query: 64  GAIFAALLGLVIGFATLRLREDYLAIVTIGTGELIRLVVNN-QDLPVGDTWVSGAFGVQS 122
             + AA  G+V+GF  LRLR DY+AIVT+G GE++R+V+ N QD+  G   +S   G++ 
Sbjct: 168 AGLLAAAFGMVLGFPVLRLRGDYIAIVTMGLGEIVRVVLQNWQDVTGGPNGIS---GIE- 223

Query: 123 YPIPLSTEPNLFFRLLMIGILTLLFAVTVFSLWRWIRNAQKLQLTDATDKTSSKQEIASR 182
                   P+LF                               L+         Q  A  
Sbjct: 224 -------RPSLF------------------------------GLSFKMVPPEGSQTFAEF 246

Query: 183 FGVGIILGLLATAIYISGVITLYNYIPKAGLMLVSLLVLAFVFWRLEYLVRSPWGRVLKA 242
           FG+           Y +    ++ Y     L+L   L+   +  R+    R P GR  +A
Sbjct: 247 FGLD----------YSADHRVIFLYF----LILALALLTNVITLRIR---RLPVGRAWEA 289

Query: 243 IREDEEIPKAMGKNVFWYKLQSLMLGGAIAGIAGAFFAWQISAIYPDNFQPQLTFDSWIM 302
           +REDE   +++G N    KL +   G   AG AG+FFA +   I P++F    +     +
Sbjct: 290 LREDEIACRSLGINPTLVKLSAFATGAMFAGFAGSFFATRQGFISPESFTFIESAVILAI 349

Query: 303 VILGGAGNNIGSILGAVIYFAYDAITREVLPKIIPLDEARLGAFRIMCIGLILMVLMIWR 362
           V+LGG G+ IG +L A++        RE            L  FR++  G  ++++M+W+
Sbjct: 350 VVLGGMGSQIGIVLAALLLVGLPEWFRE------------LQQFRMLAFGGAMVLIMLWK 397

Query: 363 PQGILGKKE 371
           P G+L  +E
Sbjct: 398 PAGLLSTRE 406


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: 512
Number of extensions: 34
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: 415
Length adjustment: 31
Effective length of query: 346
Effective length of database: 384
Effective search space:   132864
Effective search space used:   132864
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 Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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