GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_15495
          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:

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