GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gci in Salinicoccus carnicancri Crm

Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate WP_017549877.1 C792_RS0112915 galactonate dehydratase

Query= BRENDA::A9CEQ8
         (378 letters)



>NCBI__GCF_000330705.1:WP_017549877.1
          Length = 382

 Score =  151 bits (382), Expect = 3e-41
 Identities = 116/355 (32%), Positives = 169/355 (47%), Gaps = 25/355 (7%)

Query: 32  VLVEIECDDGTVGWGECL--GPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQG 89
           + +++E D G VGWGE +  G A    A V      LIG+DP + E IW  LY   R   
Sbjct: 16  LFLKVETDAGLVGWGEPVIEGKAATVKAAVIEMMETLIGRDPLEIEGIWNELY---RSGF 72

Query: 90  QRG--LSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYA-TGSFKRDNVDRVS 146
            RG  + ++A+SGID ALWDIKGK+YGA +  LLGGR R+S++ Y+  G       DR +
Sbjct: 73  YRGGPILMSAISGIDQALWDIKGKYYGAPVHELLGGRARDSIKVYSWVGG------DRPA 126

Query: 147 DNASEMAERRAEGFHACK---------IKIGFGVEEDLRVIAAVREAIGPDMRLMIDANH 197
           D      E + +G  A K         I     V+  L  + ++R + G D  + ID + 
Sbjct: 127 DVGEASLELKNQGITAVKMNATEELQYIDSYSKVDMVLERVDSIRRSCGTDFGIGIDFHG 186

Query: 198 GYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGMWQA 257
                 A  L      F   + EEP +PE  +    +     IP+A GE    ++     
Sbjct: 187 RVHKPMAKVLARELEQFRPMFIEEPALPENNENLRDIAMHTAIPIATGERMFSKWQFKTL 246

Query: 258 LSAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTPD 317
           L  G  DI+QPDL   GG +E +KI ++A    V   PH     + +A+ LQ  A     
Sbjct: 247 LQDGYADIIQPDLSHAGGITECKKIMSMAEAFDVAAAPHCPLGPIALASCLQVDATCHNA 306

Query: 318 PVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEINRDALTE 372
            ++   +   + +++ ++           E  +G V IPDGPGLGIEIN D + E
Sbjct: 307 IIQEQSLG--IHYNKGNDILDYIKDASVFEYTDGHVKIPDGPGLGIEINEDYVRE 359


Lambda     K      H
   0.321    0.138    0.431 

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: 401
Number of extensions: 13
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: 378
Length of database: 382
Length adjustment: 30
Effective length of query: 348
Effective length of database: 352
Effective search space:   122496
Effective search space used:   122496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 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