GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Lactobacillus oryzae SG293

Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate WP_034528196.1 LOSG293_RS05960 amino acid permease

Query= TCDB::M1IW84
         (556 letters)



>NCBI__GCF_000740055.1:WP_034528196.1
          Length = 498

 Score =  269 bits (687), Expect = 2e-76
 Identities = 149/398 (37%), Positives = 226/398 (56%), Gaps = 18/398 (4%)

Query: 11  TDTQPH-LRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPA-VMVVYGIIGFFVFFV 68
           T+ + H ++R L  RH+ +IA+GG IGTGLF+ SG  IS AGP   +V Y  +G  V+F+
Sbjct: 10  TELENHEVKRGLKTRHVSMIALGGCIGTGLFVASGSAISSAGPGGALVAYIAMGMMVYFL 69

Query: 69  LRAMGELLLSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWW 128
           + ++GE+  +     SF  ++A  + PA GF +GW+YWF W +T   D+       +FW 
Sbjct: 70  MTSLGEMATNMPISGSFAAYSAKYVDPALGFAMGWNYWFNWAITVAVDISTAALVIKFWL 129

Query: 129 PGLPIWVPALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSP 188
           PG+P W+ + V + ++  +N  SVR +GE EFW +LIK+  IV  + VG + +       
Sbjct: 130 PGVPGWIWSAVALVILFVINALSVRTYGETEFWLSLIKIVTIVVFLVVGLLTI----FGI 185

Query: 189 HGVHAT-IENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAI 247
            G HAT +EN       F  GF  ++S F +A F++ G ELVG  A E+ DP +++P+AI
Sbjct: 186 MGGHATGLENFTYKKAPFVGGFPAILSVFVVAGFSFQGTELVGITAGESEDPHKSVPKAI 245

Query: 248 NAVPLRVAVFYIGALLAILAVVPWRQF--------ASGESPFVTMFSLAGLAAAASVVNF 299
           N V  R+ +FYI A+  I  ++P+               SPF  +F  AGLAAAAS++N 
Sbjct: 246 NQVFWRIILFYILAIAVIALIIPYTSHDLLGSSATDVAISPFTLVFQRAGLAAAASIMNA 305

Query: 300 VVVTAAASSANSGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAPLLLTSIPL 359
           V++T+  SSANSG +++ RML+ LA EG+AP AF +  + G+P  AL+ T  +   +   
Sbjct: 306 VILTSVLSSANSGMYASTRMLYSLAHEGYAPKAFGRTTKNGIPMLALVGTTLIAAVTFIS 365

Query: 360 LYAGRSVIGAFTLVTTVSSLLFMFVWAMIIISYLVYRR 397
             AG  +   +  +   S L     W  I IS+  +RR
Sbjct: 366 SIAGPQL---YLWLVAASGLTGFIAWIGIAISHFRFRR 400


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: 692
Number of extensions: 48
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: 498
Length adjustment: 35
Effective length of query: 521
Effective length of database: 463
Effective search space:   241223
Effective search space used:   241223
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.

Links

Downloads

Related tools

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