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_15495 AO353_15495 serine/threonine protein kinase

Query= SwissProt::P0AAD8
         (443 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_15495 AO353_15495
           serine/threonine protein kinase
          Length = 433

 Score =  389 bits (998), Expect = e-112
 Identities = 210/435 (48%), Positives = 281/435 (64%), Gaps = 23/435 (5%)

Query: 9   SSQTKQSSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHR 68
           S+ T    W K DTTW LGL+GTAIGAG LF PI AG GG  P+L++ +LA+P+ F+ HR
Sbjct: 19  STATTSKGWSKHDTTWMLGLYGTAIGAGTLFLPINAGVGGFWPLLVLALLAFPMTFFAHR 78

Query: 69  ALARLCLSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWE 128
            L R  LSG   SG+ITE VEEHFG   G +IT LYFFAI P+L +Y V +TNT  +F E
Sbjct: 79  GLTRFVLSGR--SGDITEVVEEHFGIGAGKLITLLYFFAIFPILLVYSVALTNTLSSFME 136

Query: 129 NQLGFAPLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNS 188
           +QL  AP  R  ++L L+L +  ++  G+ ++VK MS LV+PF+A+L+L+ +SLIP WN 
Sbjct: 137 HQLHIAPPPRSVLSLALILGLMAIVRCGQGVIVKCMSVLVYPFVAALLLLGVSLIPNWNG 196

Query: 189 AVIDQVDLG-SLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRDF 247
           A       G  L L        T+WL I +MVFSFN SPI+S+F V +++ Y        
Sbjct: 197 AFFASASEGMPLPL-----FFKTLWLAIPVMVFSFNHSPIISAFAVDQKQRYGTQ----- 246

Query: 248 TERKCSQIISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGT 307
            E K S I++ A  +MV  VMFF FSC+  LSPA++A AKAQNI +LSYLANHF +    
Sbjct: 247 AEPKSSGILAVAHSMMVLTVMFFCFSCVLALSPADLAAAKAQNISILSYLANHFQTP--- 303

Query: 308 KTTFAITLEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLGKLNTIS 367
                  + YAA +IALVAI KSF GHY+G  EG  GL++K   +G    +    LN ++
Sbjct: 304 ------VIAYAAPLIALVAITKSFLGHYIGASEGFQGLIVK-SLRGRGRVMPTSWLNRVT 356

Query: 368 MIFIMGSTWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFV 427
            +F++ S W VA  NP+IL +IE +G P+IA LL L+PMYAIR+ PSL +Y G+  NVFV
Sbjct: 357 ALFMILSCWAVATFNPSILGMIETLGGPVIACLLFLMPMYAIRRVPSLRQYSGQASNVFV 416

Query: 428 TVIGLLTILNIVYKL 442
            +IGL+ +  I+Y +
Sbjct: 417 VLIGLIALSAIIYSV 431


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: 553
Number of extensions: 28
Number of successful extensions: 6
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: 433
Length adjustment: 32
Effective length of query: 411
Effective length of database: 401
Effective search space:   164811
Effective search space used:   164811
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