GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaC in Pseudomonas fluorescens FW300-N2C3

Align Serine transporter (characterized)
to candidate AO356_24385 AO356_24385 serine/threonine protein kinase

Query= SwissProt::P0AAD6
         (429 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_24385
          Length = 426

 Score =  550 bits (1418), Expect = e-161
 Identities = 279/428 (65%), Positives = 345/428 (80%), Gaps = 14/428 (3%)

Query: 2   ETTQTSTIASKDSRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAF 61
           ETT  +T+      S W + DT WMLGL+GTAIGAG LFLPINAG+GG  PL+I+A+LAF
Sbjct: 13  ETTVPATL------SQWSRQDTTWMLGLFGTAIGAGTLFLPINAGLGGFWPLLILALLAF 66

Query: 62  PMTFFAHRGLTRFVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAIT 121
           PMTF+AHRGLTRFVLSG++ G DITEVVEEHFG+ AG LITLLYFFAI+PILL+YSVA+T
Sbjct: 67  PMTFYAHRGLTRFVLSGRD-GADITEVVEEHFGLKAGALITLLYFFAIFPILLIYSVALT 125

Query: 122 NTVESFMSHQLGMTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLAL 181
           NTV SF+ HQL + PPPRA+LSL+LI+G++ +VR GEQ IVKAMS++V+PF+  L+ LA+
Sbjct: 126 NTVGSFLEHQLHIQPPPRAVLSLVLILGLLAVVRCGEQAIVKAMSLMVYPFIVALLFLAV 185

Query: 182 YLIPQWNGAALETLSLDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGD 241
           +LIP W+G  L T S     +    L  TLWLAIPVMVFSFNHSPIIS+FAV ++  YG 
Sbjct: 186 FLIPHWSGGILSTASTPPEPSA---LLHTLWLAIPVMVFSFNHSPIISAFAVDQKRRYGA 242

Query: 242 MAEQKCSKILAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVI 301
            AE++ S+IL+ AH++MV+ V+FFVFSCVL+LTPA LA AK QN+SILSYLANHF+ P I
Sbjct: 243 NAEERSSQILSRAHVLMVVMVLFFVFSCVLTLTPAQLAEAKAQNLSILSYLANHFSNPTI 302

Query: 302 AWMAPIIAIIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTTW 361
           A+ AP+IA +AI+KSFLGHY+GA EG  G+++KS    G+      L+R+TA FMLV  W
Sbjct: 303 AFAAPLIAFVAISKSFLGHYIGASEGLKGLIVKS----GRRPAPKTLDRLTAAFMLVVCW 358

Query: 362 IVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAIS 421
           IVATLNPSILGMIETLGGP+IA ILFLMPMYAI+KVPAM +Y G  SNVFVV++GL+AI+
Sbjct: 359 IVATLNPSILGMIETLGGPVIAAILFLMPMYAIRKVPAMARYRGQASNVFVVLVGLVAIT 418

Query: 422 AIFYSLFS 429
           A+ YSL +
Sbjct: 419 ALVYSLMA 426


Lambda     K      H
   0.328    0.140    0.416 

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: 628
Number of extensions: 30
Number of successful extensions: 4
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: 429
Length of database: 426
Length adjustment: 32
Effective length of query: 397
Effective length of database: 394
Effective search space:   156418
Effective search space used:   156418
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