GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natC in Marinobacter adhaerens HP15

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 GFF3114 HP15_3057 leucine/isoleucine/valine transporter permease subunit

Query= TCDB::Q8YY08
         (377 letters)



>FitnessBrowser__Marino:GFF3114
          Length = 423

 Score =  145 bits (365), Expect = 3e-39
 Identities = 112/364 (30%), Positives = 172/364 (47%), Gaps = 75/364 (20%)

Query: 8   LAISTATFALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLS-LKGVPLFISAIVGAI 66
           LA     + + +LGLN+  G  GL++ G++AF  +GAYT  LLS   G+  +++  +GA+
Sbjct: 118 LATLVLIYIMLALGLNVVVGLAGLLDLGYVAFYAVGAYTFALLSQYTGISFWLALPIGAL 177

Query: 67  FAALLGLVIGFATLRLREDYLAIVTIGTGELIRLVVNNQDLPVGDTWVSGAFGVQSYPIP 126
            AAL GLV+GF  LRLR DYLAIVT+G GE+IR+++NN       T   G  G+   P  
Sbjct: 178 LAALFGLVLGFPVLRLRGDYLAIVTLGFGEIIRILLNN-----WTTLTGGPNGIGGIP-- 230

Query: 127 LSTEPNLFFRLLMIGILTLLFAVTVFSLWRWIRNAQKLQLTDATDKTSSKQEIASRFGVG 186
              +P LF          + F   V                    K          FG+ 
Sbjct: 231 ---DPTLF---------GMEFGRRV--------------------KEEGNTSFHETFGIA 258

Query: 187 IILGLLATAIYISG---VITLYNYIPKAGLMLVSLLVLAFVFWRLEYLVRSPWGRVLKAI 243
                       SG   VI LY         L++L++  F    +   +R P GR  +A+
Sbjct: 259 -----------YSGEHKVIFLY---------LIALVLAVFTALVIRRFMRMPVGRAWEAL 298

Query: 244 REDEEIPKAMGKNVFWYKLQSLMLGGAIAGIAGAFFAWQISAIYPDNFQPQLTFDSWIMV 303
           REDE   +++G +    KL +  +G   AG AG  FA +   I P++F    +     +V
Sbjct: 299 REDEIAARSLGLSRTAVKLSAFTIGAFFAGFAGTVFASKQGFISPESFVFLESAIILAIV 358

Query: 304 ILGGAGNNIGSILGAVIYFAYDAITREVLPKIIPLDEARLGAFRIMCIGLILMVLMIWRP 363
           +LGG G+ IG +L A+      A+T      I+P        +R++  G  ++++M+WRP
Sbjct: 359 VLGGMGSQIGVVLAAI------AVT------ILPELAREFSEYRMLIFGAAMVLMMVWRP 406

Query: 364 QGIL 367
           QG++
Sbjct: 407 QGLM 410


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: 487
Number of extensions: 29
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 377
Length of database: 423
Length adjustment: 31
Effective length of query: 346
Effective length of database: 392
Effective search space:   135632
Effective search space used:   135632
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