GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ams in Megamonas funiformis YIT 11815

Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate WP_008539445.1 HMPREF9454_RS09460 alpha-glucosidase

Query= uniprot:A8LLL3
         (552 letters)



>NCBI__GCF_000245775.1:WP_008539445.1
          Length = 556

 Score =  320 bits (821), Expect = 7e-92
 Identities = 188/524 (35%), Positives = 280/524 (53%), Gaps = 53/524 (10%)

Query: 19  WWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKDFGYD 78
           WW+  V+YQIYP+SF DSNGDGIGD+ GI+ ++ Y+  LGV AIW+ P + SP+ D GYD
Sbjct: 6   WWQKTVVYQIYPKSFCDSNGDGIGDIPGIISKLDYLQDLGVGAIWLCPIYPSPLVDNGYD 65

Query: 79  ISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDNPKAD 138
           ISDY  V   +G++ D + LI  A    +++++DLV +HTSD+H WFEESRSS+DNPK D
Sbjct: 66  ISDYCSVAKEYGTMEDMERLISEADKRNIKIVMDLVFNHTSDKHKWFEESRSSKDNPKRD 125

Query: 139 WYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADVQDALLG 198
           WY+W D K DG+ P NW SIFGGS W  D +  QYYLH F ++QPDLN+   +V+ AL  
Sbjct: 126 WYIWRDGKEDGSAPTNWRSIFGGSAWTLDEKTNQYYLHTFASAQPDLNWENKEVRQALFD 185

Query: 199 VGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNIAPEVNPYNHQRHLYSKNQ 258
              FWLD+GV GFR+D I +    +E +D     P +   N+A       +Q  +     
Sbjct: 186 AANFWLDKGVRGFRIDAIVYIKKPSEFKD----LPVDGADNLASIAKATTYQDGI----- 236

Query: 259 PENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGETGV-HMCYAFEFLA--- 314
              L+FL +FR  + +   I  V E  D  Y  +       GE G   M + F  +    
Sbjct: 237 ---LDFLHEFREKVFDRADIFTVAE-ADGVYPSDF--DKWIGENGAFDMSFDFSHIRLGF 290

Query: 315 QEKLTAKR--------VAEVLNKVDEVASD-GWACWAFSNHDVMRHVS----RWDLTPGA 361
            E  T  +        + +   + +E   D GW    F NHD+ R  +    +   T  A
Sbjct: 291 DEDCTWHKRKSWKLIDIRKCFTEDEEATKDNGWVPVYFENHDLPRCTNYFFPQGTDTKLA 350

Query: 362 QRGMLTLLMCLRGSVCLYQGEELG-----------------LPEAEVAFDDLQDPYGIEF 404
            + + T+L+ +RG+  +Y+G+ELG                 + + E+A  D   P     
Sbjct: 351 AKFIATILLTMRGTPFIYEGQELGVTNIKWPSIKMYNDISSIGQYELALKDKLTPKEAMK 410

Query: 405 WPEYKGRDGCRTPMVWQSDNMSGGFSIHRPWLPVSTEHLGLAVAVQEEAPDALLHHYRRA 464
                 RD  R+PM W S +   GF+  RPWLP++ E+  L V  + E  +++L++Y+  
Sbjct: 411 GVWKYSRDNARSPMTWNSGS-KAGFTTGRPWLPLNDEYPKLNVETETEDENSVLNYYKNL 469

Query: 465 LAFRRAHPALVKGDISD-VTVVGDVISFLR--KDPEETVFVAIN 505
           +  R+ +PAL++GD  + ++    + ++ R  KD  E + V  N
Sbjct: 470 IKLRKQYPALIEGDYEELLSYSPGIYAYARTTKDKSERIIVIAN 513


Lambda     K      H
   0.321    0.138    0.451 

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: 880
Number of extensions: 38
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: 552
Length of database: 556
Length adjustment: 36
Effective length of query: 516
Effective length of database: 520
Effective search space:   268320
Effective search space used:   268320
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.

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