GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ams in Cronobacter condimenti 1330

Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate WP_007665535.1 BN137_RS16150 alpha-glucosidase

Query= uniprot:H3K096
         (538 letters)



>NCBI__GCF_000319285.1:WP_007665535.1
          Length = 558

 Score =  338 bits (868), Expect = 2e-97
 Identities = 199/524 (37%), Positives = 286/524 (54%), Gaps = 52/524 (9%)

Query: 7   WWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYD 66
           WW+    YQIYPRSF DS GDG+GDLNGI +KLDY+  L +D IW+ P + SP  D GYD
Sbjct: 12  WWKEATAYQIYPRSFKDSNGDGIGDLNGIIDKLDYLKDLGIDLIWICPMYPSPNDDNGYD 71

Query: 67  VSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKAD 126
           +SDY+ +   FGT+ DF  LLE  H  G+++++D V++HTSD+HPWF ESR +R NPK D
Sbjct: 72  ISDYQGIMAEFGTMADFDRLLEGVHQRGMRLILDLVVNHTSDEHPWFLESRASRDNPKRD 131

Query: 127 WFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQLD 186
           W++W D K +G  PNNW SIF GSAW  D+   QY++H F + QPD+N+ + E R A  D
Sbjct: 132 WYIWRDGK-NGAEPNNWESIFSGSAWKHDAATGQYFMHLFSSRQPDLNWENHEMRAAVYD 190

Query: 187 NMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLSR 246
            MR+WLD G+DGFR+D +     +  L D P            P+  PY     V  L+ 
Sbjct: 191 MMRWWLDKGIDGFRIDAIAHMKKEPTLSDVP-----------NPDKLPYA-PSMVAHLNY 238

Query: 247 PENLDFLKDL-RALMDEYPGTTTVGEIG--DDNPLERMAEYTAGGDKLHMAYTFDLLNM- 302
              LD++ D+ R + D Y    TVGE+   D +  E       G  +L+M + F+ + + 
Sbjct: 239 DGLLDYVDDICRNVFDHY-DIVTVGEMNGLDADHAEEWVGENRG--RLNMVFQFEHVRLW 295

Query: 303 -PHSA-----SYLREVIERFQR-LAGDAWPCWATSNHDVVRSATRWGADEDPH--AYPKV 353
            P +      + LR++   +Q+ L G  W      NHDV R  +RWG D + H       
Sbjct: 296 EPQAGLRPTPAVLRKIFTAWQQALEGKGWNALYVENHDVTRIVSRWG-DTERHWRESATC 354

Query: 354 MLAVLFSLRGSVCLYQGEELGLPEADVPFERIQD-----PYGK--------------VLW 394
           + A+ F ++G+  +YQG+E+G+   +  F  ++D      + K              V +
Sbjct: 355 IAAMYFLMQGTPFIYQGQEIGM--TNTRFASLEDFDDVSAHNKARDLREQGMSEAEIVAF 412

Query: 395 PEFKGRDGCRTPMPWTDGEQGGFSPVEPWLPMEARHLELAVSRQQDDPNATLNTVRALLA 454
               GRD  RTPM W      GFS  EPWL +   +  + V  QQ DP++ LN  R ++ 
Sbjct: 413 LTRTGRDNSRTPMQWDASPYAGFSTHEPWLKVNPNYEMINVESQQHDPHSVLNFYRQMIH 472

Query: 455 FRRSHPALFDGDL-SLVDVGDDLLGFTRQKGDETLLCVFNLTGQ 497
            R+  PAL  G   SL+D  + +  + R  GDE L+ + NL+G+
Sbjct: 473 LRKREPALIYGRYESLLDDHEQIYAYGRVLGDERLVVLCNLSGK 516


Lambda     K      H
   0.320    0.138    0.443 

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: 898
Number of extensions: 53
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 538
Length of database: 558
Length adjustment: 36
Effective length of query: 502
Effective length of database: 522
Effective search space:   262044
Effective search space used:   262044
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 (21.8 bits)
S2: 53 (25.0 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