GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malA in Klebsiella michiganensis M5al

Align 6-phospho-α-glucosidase (Pagl;CAC3426) (EC 3.2.1.122) (characterized)
to candidate BWI76_RS27540 BWI76_RS27540 glycoside hydrolase

Query= CAZy::AAK81356.1
         (445 letters)



>FitnessBrowser__Koxy:BWI76_RS27540
          Length = 459

 Score =  167 bits (422), Expect = 8e-46
 Identities = 121/467 (25%), Positives = 222/467 (47%), Gaps = 55/467 (11%)

Query: 6   ICIVGGGSRYTPDMLAMLCNQKERFPLRKIVLYDNESERQETVGNYAKILFKEYYPELEE 65
           + ++GGG   +  +   L     R  L ++V  D+ +E     G  A+ +F    P++  
Sbjct: 3   LTVLGGGGVRSAFLAKSLAYNAHRIGLTEVVFLDSSAENLAIFGEIARYVFNAIRPDIHF 62

Query: 66  VIWTTDEKEAFEDIDFALMQIRAGRLKMREKDEKISLKHGCLGQETCGAGGFAYGLRSVP 125
            + T+D   A ++  + +  +R G  + R +DE+I+L+H  LGQET GAGGFA  +RS+P
Sbjct: 63  SV-TSDPVPALKNSHYVITTLRVGGDESRIRDERIALEHNTLGQETTGAGGFAMAMRSIP 121

Query: 126 AVIDLIKSIRTYSPKCWIL-NYSNPAAIVAEA-TKRVFPNDYRIINICDMPIAIMDIYAA 183
           A+++  + I  ++ +  IL N++NP+ +V EA  K  F    R+  ICD P  ++    A
Sbjct: 122 AILNYCRLIEEHAAEDAILFNFTNPSGLVTEAIIKSGFKR--RVYGICDAPSELIRELPA 179

Query: 184 VLGLKRRDLEPKYFGLNHFGWFTHILDKKTGENYLPKLREILKTPVDVQTEPLFQEKSWK 243
           +LG   RDL  + +GLNHF WFTH   +  GE+   +L         + +  L+++ + +
Sbjct: 180 ILGCDERDLGVECYGLNHFSWFTHFTVR--GEDVTERL---------IASPDLYRKTAMQ 228

Query: 244 STFEFMSQMINDYDEYLPNTYLQYYLY-PAKMRNKENPEYTRANEVMDGNE--------- 293
               F  +++   D+ L N YL YY Y    ++  +N   TR  ++   N          
Sbjct: 229 ---YFSPELVQLCDKQLLNEYLYYYYYREVALKAIQNAPETRGEQIARINHDMREELRTV 285

Query: 294 ------------------KETYERMHKIISLGKIHGTKYELT-------SDVGCHAEYIV 328
                             +     M       K H T+  LT        D G +A   +
Sbjct: 286 DVKANPEAAFTLWMKHYLRRENSYMQNESQQEKFH-TREPLTLKQFIEEPDTGGYAGVAL 344

Query: 329 DLATAIANNTNEIFLIITENKGTINNVSKDMMVEVPCRVGSNGVEPLVVGSIPAFYKGLM 388
           D+  A+ +   +  ++   N GT++ +  D ++E+ C +  +G++P+    +P   K ++
Sbjct: 345 DILEAVNSTATKRIVVSMSNNGTLDFLRPDDVIEISCDLSKDGLKPVTPKHVPTAQKNMI 404

Query: 389 ENQYAYEKLSVDACLEGSYQKALQALVLNRTVVNTDVAKELLKDLIE 435
            +   YE+L+V A L+     A++AL+ +  V +  +AK L++  ++
Sbjct: 405 ASVKEYERLAVAAILQRDKSLAVRALMAHPLVGSYSLAKTLVEAYLD 451


Lambda     K      H
   0.319    0.136    0.406 

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: 494
Number of extensions: 27
Number of successful extensions: 4
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: 445
Length of database: 459
Length adjustment: 33
Effective length of query: 412
Effective length of database: 426
Effective search space:   175512
Effective search space used:   175512
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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