GapMind for catabolism of small carbon sources

 

Alignments for a candidate for serP1 in Pseudomonas fluorescens GW456-L13

Align Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized)
to candidate PfGW456L13_4291 Aromatic amino acid transport protein AroP

Query= TCDB::F2HQ25
         (459 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4291
          Length = 467

 Score =  291 bits (746), Expect = 2e-83
 Identities = 169/468 (36%), Positives = 258/468 (55%), Gaps = 33/468 (7%)

Query: 2   ENLQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFF 61
           + +  + E +RGL+NRHIQLIA+ G IGTGLFLG+   ++  GPS+I  Y + G   F  
Sbjct: 3   DEILRQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLI 62

Query: 62  LRTIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWL 121
           +R +GEM+  +P   SF +F  KY G   G+ + W+YW++ V V ++ELTA+G Y+QFW 
Sbjct: 63  MRQLGEMIVEEPVAGSFSHFAHKYWGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWW 122

Query: 122 PQVPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYS 181
           P+VP W+   V   L+  +N +N + FGE EFWFA+IKV AIIGMI     +        
Sbjct: 123 PEVPSWVSAAVFFVLVNLINMMNVKVFGEMEFWFAIIKVVAIIGMIALGCYM-------- 174

Query: 182 TVLSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKK 241
             L   T    AS+SN++D    FP+G    + A+  +MF+F  +E +G+TAAE   P K
Sbjct: 175 --LFSGTGGPQASVSNLWDHGGFFPNGYSGLLMAMAFIMFSFGGLELVGITAAEASEPGK 232

Query: 242 SLPKAINQIPVRILLFYVGALLAIMAIFNWHYI---------PADKSPFVMVFQLIGIKW 292
            +PKAINQ+  R+L+FYVGAL  +++++ W  +             SPFV +F LIG   
Sbjct: 233 VIPKAINQVVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYGGSPFVQIFSLIGSDT 292

Query: 293 AAALINFVVLTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMAT 352
           AA ++NFVVLT+A S  NS ++  +R +Y LA+Q D  +     KL+K G+P+ AL ++ 
Sbjct: 293 AAHILNFVVLTAALSVYNSGVYCNSRMLYGLAEQGDAPK--ALMKLNKQGVPLLALGVSA 350

Query: 353 ALSLLAPVLTLIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKSEDYNP-----KGF 407
            ++LL+ ++  +     A +   +      ++ + +   T+ ++RK           K F
Sbjct: 351 LITLLSVLVNYLAP-HEALELLFALVVASLMINWAMISLTHLKFRKIMSQQGIVPGFKSF 409

Query: 408 LTP-KPQITVPFIVAIFAIVFASLFFNADTFYPALGAIVWT-IFFGLY 453
             P    + + F+V I  ++       A  F       VW  I FG Y
Sbjct: 410 WFPFSNYLCLAFMVMIVCVMLMIPGIRASVF----AIPVWVLIIFGFY 453


Lambda     K      H
   0.329    0.141    0.434 

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: 603
Number of extensions: 39
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: 459
Length of database: 467
Length adjustment: 33
Effective length of query: 426
Effective length of database: 434
Effective search space:   184884
Effective search space used:   184884
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: 51 (24.3 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