GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Pseudomonas fluorescens FW300-N2E2

Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate Pf6N2E2_4959 S-methylmethionine permease

Query= TCDB::M1IW84
         (556 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959
          Length = 476

 Score =  266 bits (680), Expect = 1e-75
 Identities = 161/473 (34%), Positives = 253/473 (53%), Gaps = 22/473 (4%)

Query: 12  DTQPHLRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPAVMVVYGIIG-FFVFFVLR 70
           +T+   ++++  RHI ++A+GG IGTGLF+ SG T++ AGP   V+  IIG   V+ V+ 
Sbjct: 9   NTRAGFKQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALMVYMVMM 68

Query: 71  AMGELLLSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPG 130
            +GEL +      SF  +A   LGP  G+ V W YW  W V   ++  A       W+P 
Sbjct: 69  CLGELAVQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILMSRWFPD 128

Query: 131 LPIWVPALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVC--LIAVGAILVATNFVSP 188
            P+W+ + +   ++   N+ SVR F E EFW +LIKV  +V   LI  GAIL   N    
Sbjct: 129 TPVWIWSALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGLLNIDQA 188

Query: 189 HGVHATIENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAIN 248
           H +   + N   + G FPTGF+ +        FA+ G EL+G AA ET DP+R +PRAI 
Sbjct: 189 HSIG--LSNFTRE-GLFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVPRAIR 245

Query: 249 AVPLRVAVFYIGALLAILAVVPWRQFASGESPFVTMFSLAGLAAAASVVNFVVVTAAASS 308
              LR+AVF++G +  +  ++P  Q    ESPFVT+F+  G+  +A ++NFV+++A  S+
Sbjct: 246 TTVLRLAVFFVGTIFVLATLLPREQAGLVESPFVTVFTYIGIPYSADIMNFVIISALLSA 305

Query: 309 ANSGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLT----APLLLTSIPLLYAGR 364
           ANSG ++  RML+ L+D+GH P  F  L R G P  A++++    A  LL+S+   +A  
Sbjct: 306 ANSGLYAASRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSV---FAAD 362

Query: 365 SVIGAFTLVTTVSSLLFMFVWAMIIISYLVYRRRHPQRHTD---SVYKMPGGVVMCWAVL 421
           ++   +  + ++S L  + VW  I  S + +RR +     D     +++ G   +    L
Sbjct: 363 TI---YLALVSISGLAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPWVPLGAL 419

Query: 422 VFFAFVIWTLTTETETATALAWFPLWFVLLA--VGWLVTQRRQSRRSFGFHCQ 472
           V  +     +  + E   AL +F L F+     V ++  + R+ R S  F  Q
Sbjct: 420 VCCSLACIGIAFDPEQRVAL-YFGLPFIAWCYFVYYITRKSRERRLSVAFVAQ 471


Lambda     K      H
   0.328    0.140    0.442 

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: 634
Number of extensions: 28
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: 556
Length of database: 476
Length adjustment: 35
Effective length of query: 521
Effective length of database: 441
Effective search space:   229761
Effective search space used:   229761
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: 52 (24.6 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