Alignments for a candidate for susB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Klebsiella michiganensis M5al

Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate BWI76_RS03235 BWI76_RS03235 alpha-glycosidase

Query= BRENDA::P21517
         (604 letters)



>FitnessBrowser__Koxy:BWI76_RS03235
          Length = 598

 Score =  198 bits (503), Expect = 6e-55
 Identities = 139/428 (32%), Positives = 205/428 (47%), Gaps = 68/428 (15%)

Query: 117 PQWAADQIFYQIFPDRFARSLPREAEQDHVYYHHAAGQEIILRDWDEPVTAQAGGSTFYG 176
           P+W    I+YQIFP+RF    P  + ++             ++ W  P  ++     F G
Sbjct: 152 PEWVKKTIWYQIFPERFCNGDPSISPEN-------------VQPWGTPPDSK----NFMG 194

Query: 177 GDLDGISEKLPYLKKLGVTALYLNPVFKAPSVHKYDTEDYRHVDPQFGGDGALLRLRHNT 236
           GDL GI  KL YL+ LGV  LYL P+F A + HKYDT DY +VDP FGG+     L    
Sbjct: 195 GDLQGIINKLDYLQDLGVNGLYLCPIFTANASHKYDTVDYFNVDPHFGGNDRFKELVQKA 254

Query: 237 QQLGMRLVLDGVFNHSGD-SHAWFDRHNRGTGGACHNPESPWRDWYSF-------SDDGT 288
            Q GM+++LD VFNH G+ S  W D    G        +SP+ DW+         S D  
Sbjct: 255 HQRGMKVMLDAVFNHIGNQSPLWLDVVKNG-------DKSPYADWFWIKKFPVYPSGDKN 307

Query: 289 ALDWLGY--------ASLPKLDYQSESLVNEIYRGEDSIVRHWLKAPWNMDGWRLDVVHM 340
             D+  +          +PKL+ ++ +  + + +    + R+W++  +++DGWRLDV   
Sbjct: 308 EWDFRNFNYETFGNVIEMPKLNTENPACRDYLLQ----VARYWIE-EFDIDGWRLDVA-- 360

Query: 341 LGEAGGARNNMQHV--AGITEAAKETQPEAYIVGEHFGDARQWLQADVEDAAMNYRGFTF 398
                   N + H          K  +P+ YI+GE + +   WL+ D  D+ MNY     
Sbjct: 361 --------NEVDHEFWRAFRRTVKSIKPDCYILGEIWHEGMPWLRGDQFDSLMNY----- 407

Query: 399 PLWGFLANTDISYDPQQIDAQTCMAWMDNYRAGLSHQQQLRMFNQLDSHDTARFKTLLGR 458
           PL    A TD  +  Q  D +T +  + +            MFN L+SHDT+R  +L G 
Sbjct: 408 PL--MQATTDY-FALQAYDKKTFIDIVTHAYLCYPRNVNEVMFNLLESHDTSRLLSLCGN 464

Query: 459 DIARLPLAVVWLFTWPGVPCIYYGDEVGLDGK---NDPFCRKPFPWQVEKQDTALFALYQ 515
           D  +  LA +++F+  G PCIYYG EVG++G         RK   W  +KQD    +  +
Sbjct: 465 DKRKARLAYLFMFSQVGSPCIYYGSEVGMNGSRAMGSEDNRKCMIWDEQKQDLEFKSFIK 524

Query: 516 RMIALRKK 523
            +I  RKK
Sbjct: 525 DLILWRKK 532


Lambda     K      H
   0.322    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: 1126
Number of extensions: 68
Number of successful extensions: 6
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: 604
Length of database: 598
Length adjustment: 37
Effective length of query: 567
Effective length of database: 561
Effective search space:   318087
Effective search space used:   318087
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources