GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ascB in Marivita geojedonensis DPG-138

Align 6-P-β-glucosidase (CelF;CelD;LicH;BSU38560) (EC 3.2.1.86) (characterized)
to candidate WP_085638927.1 MGEO_RS13965 alpha-glucosidase/alpha-galactosidase

Query= CAZy::CAA90288.1
         (442 letters)



>NCBI__GCF_002115805.1:WP_085638927.1
          Length = 446

 Score =  127 bits (320), Expect = 5e-34
 Identities = 123/455 (27%), Positives = 208/455 (45%), Gaps = 42/455 (9%)

Query: 6   KIVTIGGGSSYTPELVEGFIKRYDELPVRELWLVDIPEGEEKLNIVGTLAKRMVEKAGVP 65
           +I  IG GS+   + + G +  +  L      L+DI   E++L     +A++++  +G  
Sbjct: 3   RIAFIGAGSTIFMKNIVGDVLHFPALEGATFALMDI--NEQRLEESALVARKLIAASGRS 60

Query: 66  IDIHLTLDRRKALKDADFVTTQFRVGLLQ-ARAKDERIPLKYGV---IGQETNGPGGLFK 121
             +  T D+R+AL  ADFV T F++G  + +   D  IP +YG+   IG +T G GG+ +
Sbjct: 61  AQVETTTDQRRALAGADFVVTAFQIGGYEPSTVIDFDIPKQYGLRQTIG-DTLGVGGIMR 119

Query: 122 GLRTIPVILEIAKDIEELCPNAWLVNFTNPAGMVTEALLRYSNLKKVVGLCNVPIGIKMG 181
           GLRT+P +  +A D+ ELCP+A L+ + NP  + T A+       K VGLC+        
Sbjct: 120 GLRTVPHLWRVAADMAELCPDATLLQYVNPMAINTWAIAESYPGVKQVGLCHSVQNTVEE 179

Query: 182 VAKALDVDVDRVEVQFAGLNHMVFGLDVFLDGVSVKEQVIEA--MGD-PKNAMTMKNISG 238
           +A  LD+    +  + AG+NH+ F LD+   G S+   + E   +G  PK  + M   + 
Sbjct: 180 LAHDLDLPKGEIRYRVAGVNHVAFFLDLTHKGKSLYPALREGYRVGSLPKPPLLMPRCAN 239

Query: 239 -AEWEPDFLKALNVIPCGYHRYYFKTKEMLEHELEASQ--TEGTRAEVVQKVEKELFELY 295
              +E              H  YF T E  EH  E      +  R +++      L E  
Sbjct: 240 KVRYE-----------VMEHLGYFCT-ESSEHLAEYVPWFIKSGREDLIDAFSVPLDEYP 287

Query: 296 K----------DPNLAIK-PPQLEKRGGAYYSDAACNLISSIYNDKHDIQPVNTINNGAI 344
           K          D   A +   Q++ R    ++    N  + + N  + I   N  N G  
Sbjct: 288 KRCIEQMADWADQAKAYRTADQIDFRKSHEFAAEIMN--AMVTNQPYTIYG-NLSNRGQA 344

Query: 345 ASIPDDSAVEVNCVMTKTGPKPIAVGDLPVSVRGLVQQIKSFERVAAEAAVTGDYQTALL 404
             +P  +AVEV C++   G +P  + D+P  +  L++   + + +   A V  D +    
Sbjct: 345 PQLPSGAAVEVPCMVDANGIQPTVIDDIPPQLVALMRTQINVQELVVRALVDEDIEHVYH 404

Query: 405 AMTINPLVPSDTVAKQI---LDEMLEAHKAYLPQF 436
           A  ++P   ++   +QI   + ++L AH   LP+F
Sbjct: 405 AAMMDPHTAAELDLRQIRSLVTDLLAAHGDMLPEF 439


Lambda     K      H
   0.318    0.137    0.394 

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: 27
Number of successful extensions: 3
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: 442
Length of database: 446
Length adjustment: 32
Effective length of query: 410
Effective length of database: 414
Effective search space:   169740
Effective search space used:   169740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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