GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Thermoactinomyces daqus H-18

Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate WP_033100257.1 JG50_RS0106285 amino acid permease

Query= TCDB::M1IW84
         (556 letters)



>NCBI__GCF_000763315.1:WP_033100257.1
          Length = 446

 Score =  275 bits (704), Expect = 2e-78
 Identities = 156/453 (34%), Positives = 251/453 (55%), Gaps = 21/453 (4%)

Query: 16  HLRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPAVMVVYGIIGFFVFFVLRAMGEL 75
           HL++ L  RH+Q++A+GGAIG G+F GS  TIS AGP V+  Y + G  ++ V+ AM E+
Sbjct: 4   HLQKQLLPRHVQMMALGGAIGAGIFQGSAETISAAGPGVIFSYALAGILLYIVMSAMAEM 63

Query: 76  LL--SNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPGLPI 133
            L  +  + +  V  A    G    F +GW Y+  WV+    ++V   ++ ++W+  +P+
Sbjct: 64  ALGFAGTDLRGLVHKA---FGTRVSFILGWLYFIQWVLVMAVEIVTAGTFLQYWF-SVPV 119

Query: 134 WVPALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSPHGVHA 193
           W+ +L+   +I+A+NLFSVR FGE+E+W   +K+  ++  + +GA+L+    + P     
Sbjct: 120 WLLSLIVTLVIIAINLFSVRLFGEIEYWLTSVKIVTLIVFVILGALLLFG--IIPSAQAP 177

Query: 194 TIENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAINAVPLR 253
            + N     GFFP G+ GV+S   I  F+Y G E++G    E  D ++TLPR I  V LR
Sbjct: 178 GLTNYRVHGGFFPLGWQGVLSSLLIVIFSYGGTEMIGLTITEMKDAKKTLPRVIKGVILR 237

Query: 254 VAVFYIGALLAILAVVPWRQFASGESPFVTMFSLAGLAAAASVVNFVVVTAAASSANSGF 313
           + +FY+  LL I  ++PW Q  S  SPFV + S  GL   A+++NF+++TA  S+ANSG 
Sbjct: 238 ICLFYVLPLLIITGLIPWDQVKSSGSPFVEVLSAVGLKGVANIMNFILLTAVISAANSGM 297

Query: 314 FSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAP-LLLTSIPLLYAGRSVIGAFTL 372
           ++T RML+ LA E  APA F +L + GVP  AL  ++  L L S+    A  SV   F  
Sbjct: 298 YATTRMLYSLAGEKEAPAFFTRLGKRGVPIYALAASSVCLFLGSLVAFIAPESV---FQY 354

Query: 373 VTTVSSLLFMFVWAMIIISYLVYRRRHPQRHTD---SVYKMPGGVVMCWAVLVFFAFVIW 429
           +  +     +  W +I +S+L  R ++ +R  D   S +    G+ +    +V  A +I+
Sbjct: 355 LMGIPGYTVILTWILICLSHLKLRGKY-ERTPDFRLSFFPFTTGITL----IVLAAIMIF 409

Query: 430 TLTTETETATALAWFPLWFVL-LAVGWLVTQRR 461
            L +       + +  +  VL +A  WL   +R
Sbjct: 410 VLLSPKNLINTIVYLAIILVLTIASQWLKPNQR 442


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: 525
Number of extensions: 29
Number of successful extensions: 5
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: 446
Length adjustment: 34
Effective length of query: 522
Effective length of database: 412
Effective search space:   215064
Effective search space used:   215064
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 24 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