GapMind for catabolism of small carbon sources

 

Aligments for a candidate for treC in Dyella japonica UNC79MFTsu3.2

Align trehalose-6-phosphate hydrolase (TreA;BSU07810) (EC 3.2.1.93) (characterized)
to candidate N515DRAFT_3393 N515DRAFT_3393 alpha-glucosidase

Query= CAZy::CAB12610.1
         (561 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3393 N515DRAFT_3393
           alpha-glucosidase
          Length = 541

 Score =  316 bits (809), Expect = 2e-90
 Identities = 186/539 (34%), Positives = 282/539 (52%), Gaps = 58/539 (10%)

Query: 5   QTPWWKKAVVYQIYPKSFNDTTGNGVGDLNGIIEKLDYLKTLQVDVLWLTPIYDSPQHDN 64
           +TPWW+ AV+YQIYP+SF DT G+GVGDL GI+E+LDY+  L VD +W+ P + SP  D 
Sbjct: 3   ETPWWRGAVIYQIYPRSFLDTDGDGVGDLPGIVERLDYIAGLGVDAIWIAPFFRSPMADF 62

Query: 65  GYDIRDYYSIYPEYGTMEDFERLVSEAHKRDLKVVMDLVVNHTSTEHKWFREAISSIDSP 124
           GYDI DY ++ P +GT++DF+RL+++AH   LKV++D V++HTS +H+WF+E+ +S D+P
Sbjct: 63  GYDIADYRAVDPLFGTIDDFDRLLAKAHALGLKVMIDQVLSHTSDQHEWFKESRASRDNP 122

Query: 125 YRDFYIWKKPQENGSVPTNWESKFGGSAWELDEASGQYYLHLFDVTQADLNWENEEVRKH 184
             D+Y+W   +++G+ P NW S FGG AW+ +   GQYYLH F  +Q DLN+ + +V++ 
Sbjct: 123 KADWYVWADARDDGTPPNNWMSLFGGVAWQWEPRRGQYYLHNFLTSQPDLNFHHPDVQRA 182

Query: 185 VYDMMHFWFEKGIDGFRLDVINLISKDQRF------PNAEEGDGRSFYTDGPRVHE---- 234
           V D + FW +KG+DG RLD IN    D++       P A    GR F  D P   +    
Sbjct: 183 VLDNVQFWLDKGVDGLRLDAINFCFHDRQLRDNPPKPQAMR-VGRGFSPDNPYAFQYHYY 241

Query: 235 ---------FLHEMNEKVFSHYDSMTVGEMSS-TTVDHCIRYTNPDNKELDMTFSFHHLK 284
                    FL E+   +  +  +  +GE+SS  ++     YT      L M +SF  L 
Sbjct: 242 NNTQPENLAFLEELRGLLDRYPGAAALGEISSEDSLATMAEYTT--GHRLHMGYSFELLT 299

Query: 285 VDYPNGEKWALAPFDFLKLKEILSDWQTGMHAGGGWNALFWCNHDQPRVVSRYG----DD 340
            D           F    ++  +   +  M    GW      NHD  RV+SR+G     +
Sbjct: 300 AD-----------FSAAYIRGTVERLEAQMTE--GWPCWAISNHDVERVLSRWGREARGN 346

Query: 341 GAYRVKSAKMLATAIHMMQGTPYIYQGEELGMTNPKFTDISSYRDVESLNMYHAFKEKGM 400
           G   V+ A +L   +  ++G+  +YQGEEL +T             E+   Y A ++   
Sbjct: 347 GDASVRLANLLTAMVCSLRGSVCVYQGEELALT-------------EAEVPYEALQD--- 390

Query: 401 ADQDITAILQAKSRDNSRTPVQWDATENGGFTTGTPWIPVAGNYREINAEAALRDQNSVF 460
               IT     K RD  RTP+ WD + N GF++G PW+PV   +R +       D  S  
Sbjct: 391 -PYGITFWPNFKGRDGCRTPMPWDESANAGFSSGAPWLPVPAGHRALAVSRQELDPASAL 449

Query: 461 YHYQKLIQIRKMYDIVTEGTYEIIAKDDPNIFAYLRHGSNEKLLVINNFYGTEAAFTLP 519
           + ++  +Q R+    +  G    +   +P + A+ R  + E +L   N      A  LP
Sbjct: 450 HGFRGFMQWRQAQPELRWGAIGFLDTPEP-VLAFTRTHAGETVLAAFNLGSAPVAVALP 507


Lambda     K      H
   0.318    0.135    0.423 

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: 897
Number of extensions: 50
Number of successful extensions: 4
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: 561
Length of database: 541
Length adjustment: 36
Effective length of query: 525
Effective length of database: 505
Effective search space:   265125
Effective search space used:   265125
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: 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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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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