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_033101984.1 JG50_RS0115245 amino acid permease

Query= TCDB::M1IW84
         (556 letters)



>NCBI__GCF_000763315.1:WP_033101984.1
          Length = 484

 Score =  254 bits (650), Expect = 4e-72
 Identities = 162/461 (35%), Positives = 256/461 (55%), Gaps = 25/461 (5%)

Query: 15  PHLRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPA-VMVVYGIIGFFVFFVLRAMG 73
           P L+R L  RH+ +IAIGG+IGTG+F+ SG +IS AGP   +V Y  IG  V+F++ ++G
Sbjct: 8   PELKRGLKARHLSMIAIGGSIGTGVFLASGASISEAGPGGALVAYLAIGIMVYFLMTSLG 67

Query: 74  ELLLSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPGLPI 133
           E+        SF  +A   + PA GF +GW+YW+ W +T   +L A +    +W+P  P 
Sbjct: 68  EMATFMPVAGSFSTYAGRFVDPALGFAMGWNYWYNWAITIAVELSAGSLIMDYWFPHSPS 127

Query: 134 WVPALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSPHGVHA 193
            + + + + L+  +N  SV+ +GE E+WF+ IKVA ++  I +G +++   F    G   
Sbjct: 128 ILWSALFLLLMFGLNALSVKGYGESEYWFSFIKVATVIIFIVIGLLMI---FGIMGGEAI 184

Query: 194 TIENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAINAVPLR 253
             +N   ++  F  G+LG++S F IA F++ G ELVG AA E+ +PR+ +P+AI  V  R
Sbjct: 185 GFKNFTINDAPFHHGWLGILSVFMIAGFSFQGTELVGVAAGESENPRKNVPKAIRQVFWR 244

Query: 254 VAVFYIGALLAILAVVPWR--QFASGE------SPFVTMFSLAGLAAAASVVNFVVVTAA 305
           + +FY  A+L +  V+P+       G+      SPF  +F  AGLA AASV+N V++T+ 
Sbjct: 245 ILLFYALAILVMGLVLPYTNPNLVGGDVNQIAKSPFTIIFEKAGLAFAASVMNAVILTSV 304

Query: 306 ASSANSGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAPLLLTSIPLLYAGRS 365
            S+ NSG +++ RML+ +A EG AP  F ++NR GVP  ALLLT  +   +      G+ 
Sbjct: 305 LSAGNSGMYASTRMLWQMAKEGKAPKLFAKVNRRGVPVFALLLTTAVGAVAFLASLVGQG 364

Query: 366 VIGAFTLVTTVSSLLFMFVWAMIIISYLVYRRRHPQRHTD---SVYK---MPGG----VV 415
            I  +  +   S L     W  I IS+  +RR +  +  D    VY+    P G    +V
Sbjct: 365 KI--YIWLLNASGLSGFIAWLGIAISHYRFRRAYVAQGRDLNHLVYRAKWFPFGPLFALV 422

Query: 416 MCWAVLVFFAFVIWTLTTETETATALAWFPL-WFVLLAVGW 455
           +C  V+V   +  +T  T       +++  L  F+LL +G+
Sbjct: 423 LCVIVIVGQNYQAFTGNTIDWNGILVSYIGLPLFILLWLGY 463


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: 675
Number of extensions: 40
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: 484
Length adjustment: 35
Effective length of query: 521
Effective length of database: 449
Effective search space:   233929
Effective search space used:   233929
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