GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tyrP in Shewanella sp. ANA-3

Align Tyrosine permease (characterized)
to candidate 7024668 Shewana3_1846 aromatic amino acid transporter (RefSeq)

Query= TCDB::P0AAD4
         (403 letters)



>lcl|FitnessBrowser__ANA3:7024668 Shewana3_1846 aromatic amino acid
           transporter (RefSeq)
          Length = 395

 Score =  397 bits (1021), Expect = e-115
 Identities = 194/396 (48%), Positives = 276/396 (69%), Gaps = 8/396 (2%)

Query: 2   KNRTLGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHV 61
           +N+  GS+ ++AGTTIGAGMLA+P+A+AG+GF V+ ++++ LWALM YTALL++E++Q  
Sbjct: 3   QNKFFGSLLLIAGTTIGAGMLALPIASAGLGFGVSSLIMLLLWALMAYTALLMVEIHQFA 62

Query: 62  PADTGLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSAT 121
           P+D  L  LA+  LG  GQ +   ++MFL+YAL AAYI+G GE +   ++ W G+ +   
Sbjct: 63  PSDASLNQLARTLLGAKGQVIASIALMFLLYALCAAYIAGGGEQVNQKLNAWLGLELPTQ 122

Query: 122 AGVLLFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQG 181
           AG + FT + G +V +GT  VDL NR LFS KII L++ML LLLP +   +LL LPL+QG
Sbjct: 123 AGAIFFTLLIGTIVGLGTHCVDLINRVLFSLKIIALILMLALLLPQVEGTHLLELPLEQG 182

Query: 182 LALSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATLGSID 241
           L +SAIPVIFTSFGFHGS+PS+V Y+   ++ LR + ++GSA+PL+ Y+ WQ+ + G + 
Sbjct: 183 LIVSAIPVIFTSFGFHGSIPSVVRYLGVEVKSLRKIMLLGSALPLLIYLLWQLGSQGVLS 242

Query: 242 STTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDYLADL 301
            +  M     +  L+G +  L  ++ S ++  A+ +FADLALATSFLGV+LGLFD++A  
Sbjct: 243 QSQLM----TNQSLSGFINQLASVLHSQYLSSAISVFADLALATSFLGVSLGLFDFMAAN 298

Query: 302 FQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTWQSR- 360
            ++ +   GR  T AITF+PPL FALFYP+GF+ ALGYA +AL +LA+ +P  + W  R 
Sbjct: 299 LRQQDNAAGRSITAAITFVPPLGFALFYPQGFITALGYAAIALVILAIFLPVTMVWVQRQ 358

Query: 361 ---KHNPQAGYRVKGGRPALVVVFLCGIAVIGVQFL 393
              K N   GYRV GG+  L++  LCG+AVIG Q L
Sbjct: 359 TRDKANLPQGYRVAGGKLGLLLAMLCGVAVIGAQLL 394


Lambda     K      H
   0.329    0.143    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: 443
Number of extensions: 16
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: 403
Length of database: 395
Length adjustment: 31
Effective length of query: 372
Effective length of database: 364
Effective search space:   135408
Effective search space used:   135408
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 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 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