GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tdcC in Pseudomonas fluorescens FW300-N2E3

Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate AO353_21595 AO353_21595 serine/threonine protein kinase

Query= SwissProt::P0AAD8
         (443 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_21595 AO353_21595
           serine/threonine protein kinase
          Length = 426

 Score =  401 bits (1030), Expect = e-116
 Identities = 208/429 (48%), Positives = 287/429 (66%), Gaps = 26/429 (6%)

Query: 15  SSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHRALARLC 74
           SSW + DTTW LGLFGTAIGAG LF PI AG GG  P+L++ +LA+P+ FY HR L R  
Sbjct: 21  SSWNRHDTTWMLGLFGTAIGAGTLFLPINAGLGGFWPLLILALLAFPMTFYAHRGLTRFV 80

Query: 75  LSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWENQLGFA 134
           LSG     +ITE VEEHFG   G +IT LYFFAI P+L IY V +TNT  +F E+QL   
Sbjct: 81  LSG-RAGADITEVVEEHFGIKAGALITLLYFFAIFPILLIYSVALTNTVGSFLEHQLHIM 139

Query: 135 PLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNSAVIDQV 194
           P  R  ++  L+L +  V+  G+ ++VK MS +V+PFI +L+ +++ LIP+WN  +++  
Sbjct: 140 PPPRAILSFVLILGLLAVVRCGEQMIVKAMSLMVYPFIVALLFLAVFLIPHWNGGILETA 199

Query: 195 DLGSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRDFTERKCSQ 254
                +L     +L T+WL I +MVFSFN SPI+S+F V ++  Y         E + SQ
Sbjct: 200 S----TLPEPSALLHTLWLAIPVMVFSFNHSPIISAFAVDQKRRYGA-----HAEERSSQ 250

Query: 255 IISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGTKTTFAIT 314
           I+SRA  LMV +V+FF FSC+ TLSPA +AEAKAQN+ +LSYLANHF++          T
Sbjct: 251 ILSRAHTLMVVMVLFFVFSCVLTLSPAQLAEAKAQNLSILSYLANHFSNP---------T 301

Query: 315 LEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYK-GDKTKVSLGKLNTISMIFIMG 373
           + +AA +IA VAI KSF GHY+G  EGL GL++K G +   KT      L+ ++  F++ 
Sbjct: 302 IAFAAPLIAFVAISKSFLGHYIGASEGLKGLIVKSGRRPAPKT------LDRMTAAFMLV 355

Query: 374 STWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFVTVIGLL 433
             W+VA  NP+IL +IE +G P+IA++L L+PMYAIRK P++A+YRG+  NVFVT++GL+
Sbjct: 356 VCWIVATLNPSILGMIETLGGPVIAAILFLMPMYAIRKVPAMARYRGQASNVFVTLVGLV 415

Query: 434 TILNIVYKL 442
            I  ++Y L
Sbjct: 416 AISALIYSL 424


Lambda     K      H
   0.328    0.141    0.430 

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: 517
Number of extensions: 28
Number of successful extensions: 7
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: 443
Length of database: 426
Length adjustment: 32
Effective length of query: 411
Effective length of database: 394
Effective search space:   161934
Effective search space used:   161934
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