GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natC in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_4609 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= TCDB::Q8YY08
         (377 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4609
          Length = 418

 Score = 92.0 bits (227), Expect = 3e-23
 Identities = 57/164 (34%), Positives = 89/164 (54%), Gaps = 13/164 (7%)

Query: 205 YNYIPKA-GLMLVSLLVLAFVFWRLEYLVRSPWGRVLKAIREDEEIPKAMGKNVFWYKLQ 263
           YN I K   L LV+LL+     + +  L+R P GR  +A+REDE   +A+G N    KL 
Sbjct: 256 YNSINKVIFLYLVALLLALGALFVINRLLRMPLGRAWEALREDEIACRALGLNPTVIKLS 315

Query: 264 SLMLGGAIAGIAGAFFAWQISAIYPDNFQPQLTFDSWIMVILGGAGNNIGSILGAVIYFA 323
           +  LG + AG AG+FFA +   + P++F    +     +V+LGG G+ +G IL AV+   
Sbjct: 316 AFTLGASFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAVVMIL 375

Query: 324 YDAITREVLPKIIPLDEARLGAFRIMCIGLILMVLMIWRPQGIL 367
              + RE               +R++  G +++++MIWRPQG+L
Sbjct: 376 LPEMMRE------------FSEYRMLMFGALMVLMMIWRPQGLL 407



 Score = 81.6 bits (200), Expect = 4e-20
 Identities = 55/170 (32%), Positives = 88/170 (51%), Gaps = 18/170 (10%)

Query: 8   LAISTATFALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLS-LKGVPLFISAIVGAI 66
           +A     + +  LGLN+  G  GL++ G++ F  +GAY+  LLS   G+  +I   +  +
Sbjct: 116 IATLVLIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYYGLSFWICLPIAGL 175

Query: 67  FAALLGLVIGFATLRLREDYLAIVTIGTGELIRLVVNN-QDLPVGDTWVS---------- 115
            AA  G ++GF  LRLR DYLAIVT+G GE+IRL + N   L  G   +S          
Sbjct: 176 MAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTGLTGGPNGISNIEKPTFFGL 235

Query: 116 -----GAFGVQSYPIPLSTEPNLFFRLLMIGILTLLFAV-TVFSLWRWIR 159
                 A G+Q++      E N   +++ + ++ LL A+  +F + R +R
Sbjct: 236 TFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALGALFVINRLLR 285


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: 499
Number of extensions: 30
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: 418
Length adjustment: 31
Effective length of query: 346
Effective length of database: 387
Effective search space:   133902
Effective search space used:   133902
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 (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