GapMind for catabolism of small carbon sources

 

Aligments for a candidate for serP1 in Pseudomonas putida KT2440

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 PP_4840 PP_4840 D-alanine, beta-alanine, D-serine, glycine permease

Query= TCDB::F2HQ25
         (459 letters)



>lcl|FitnessBrowser__Putida:PP_4840 PP_4840 D-alanine, beta-alanine,
           D-serine, glycine permease
          Length = 468

 Score =  355 bits (910), Expect = e-102
 Identities = 184/441 (41%), Positives = 270/441 (61%), Gaps = 12/441 (2%)

Query: 11  QRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEMLY 70
           QR L NRHIQLIAI G IGTGLF+G+GKTI + GPS+IF Y++IG  +FF +R +GE+L 
Sbjct: 15  QRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELLL 74

Query: 71  NDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVPLWLIE 130
           ++ +  SF++F     G   GYFT W+YW   V   I+++ AI  Y QFW P +P W+  
Sbjct: 75  SNLNYKSFIDFSADLLGPWAGYFTGWTYWFCWVVTGIADVVAIAAYTQFWFPDLPQWIPA 134

Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVLSGKTVH 190
           +  + LL  LN +  + FGE EFWFA++K+ AI+G++ T + +V   F   T  SG+T  
Sbjct: 135 LTCVGLLLSLNLVTVKMFGELEFWFALVKIVAILGLVATGLYMVITGF---TSPSGRT-- 189

Query: 191 DSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQI 250
             A L+N+++   +FPHG   F    Q+ +FAF  +E +G TAAE  NP+++LP+AIN I
Sbjct: 190 --AQLANLWNDGGMFPHGLMGFFAGFQIAVFAFVGIELVGTTAAEAKNPERTLPRAINSI 247

Query: 251 PVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLTSAASALN 310
           P+RI++FYV AL+AIMA+  W  +   KSPFV +F L G+  AA++INFVVLTSAAS+ N
Sbjct: 248 PIRIIVFYVLALIAIMAVTPWRDVVPGKSPFVELFVLAGLPAAASIINFVVLTSAASSAN 307

Query: 311 SSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMA-TALSLLAPVLTLIPQIKN 369
           S +FS +R +Y L+Q+ D  +   F KLS   +P N LY + T L L A ++ L+P +  
Sbjct: 308 SGVFSTSRMLYGLSQEGDAPK--AFEKLSSRSVPANGLYFSCTCLLLGAVLIYLVPNVVE 365

Query: 370 AFDFAASCTTNLFLVVYFITLYTYWQYRKSED--YNPKGFLTPKPQITVPFIVAIFAIVF 427
           AF    + +  LF+ V+ + L +Y +YRK     +    +  P  +      ++ FA + 
Sbjct: 366 AFTLVTTVSAVLFMFVWTLILLSYLKYRKDRAALHQASNYKMPGGRFMCYVCLSFFAFIL 425

Query: 428 ASLFFNADTFYPALGAIVWTI 448
             L   ADT    +   +W +
Sbjct: 426 VLLSLEADTRSALVVTPIWFV 446


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: 624
Number of extensions: 36
Number of successful extensions: 5
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: 468
Length adjustment: 33
Effective length of query: 426
Effective length of database: 435
Effective search space:   185310
Effective search space used:   185310
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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