GapMind for catabolism of small carbon sources

 

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

Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate AO356_15120 AO356_15120 amino acid transporter

Query= TCDB::M1IW84
         (556 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_15120
          Length = 476

 Score =  268 bits (685), Expect = 3e-76
 Identities = 146/396 (36%), Positives = 225/396 (56%), Gaps = 16/396 (4%)

Query: 11  TDTQPHLRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPAVMVVYGIIG-FFVFFVL 69
           T+T+   ++++  RHI ++A+GG IGTGLF+ SG T++ AGP   V+  IIG   V+ V+
Sbjct: 8   TNTRTGFKQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALMVYMVM 67

Query: 70  RAMGELLLSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWP 129
             +GEL +      SF  +A   LGP  G+ V W YW  W V   ++  A       W+P
Sbjct: 68  MCLGELAVQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILMSRWFP 127

Query: 130 GLPIWVPALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVC--LIAVGAILVATNFVS 187
             P+W+ + +   ++   N+ SVR F E EFW +LIKV  +V   LI  GAIL   N   
Sbjct: 128 DTPVWIWSALFAGVVFLTNVVSVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGLLNIDQ 187

Query: 188 PHGVHATIENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAI 247
            H +   + N   + G FPTGF+ +        FA+ G EL+G AA ET DP+R +PRAI
Sbjct: 188 AHSIG--LSNFTRE-GLFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVPRAI 244

Query: 248 NAVPLRVAVFYIGALLAILAVVPWRQFASGESPFVTMFSLAGLAAAASVVNFVVVTAAAS 307
               LR+AVF++G +  +  ++P  Q    ESPFVT+F+  G+  +A ++NFV+++A  S
Sbjct: 245 RTTVLRLAVFFVGTIFVLATLLPREQAGLVESPFVTVFTYIGIPYSADIMNFVIISALLS 304

Query: 308 SANSGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLT----APLLLTSIPLLYAG 363
           +ANSG ++  RML+ L+D+GH P  F  L R G P  A++++    A  LL+S+   +A 
Sbjct: 305 AANSGLYAASRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSV---FAA 361

Query: 364 RSVIGAFTLVTTVSSLLFMFVWAMIIISYLVYRRRH 399
            ++   +  + ++S L  + VW  I  S + +RR +
Sbjct: 362 DTI---YLALVSISGLAVVVVWMSIAASQIAFRRHY 394


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: 631
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