GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Desulfovibrio vulgaris Miyazaki F

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 8500245 DvMF_1002 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__Miya:8500245
          Length = 491

 Score =  188 bits (478), Expect = 3e-52
 Identities = 135/417 (32%), Positives = 208/417 (49%), Gaps = 36/417 (8%)

Query: 25  PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84
           P+V   AE + + D +G  Y+D    +     GH HP++ AA++ QL K++HT    L  
Sbjct: 50  PLVIGAAEGNRLTDTDGVSYLDGVSSLWTNVHGHRHPRLDAAIRAQLDKVAHTTLLGLGS 109

Query: 85  EPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIA----RAATGRAG-------VI 133
           EP IELA  +A   P    +      SGS +VE A+KIA    R A    G        +
Sbjct: 110 EPSIELAARLAAIAPQGLTR-VFYSDSGSTSVEVALKIAFQFHRQAPAHLGGDARRTRFL 168

Query: 134 AFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPC------ELHGVSEDDSIAS 187
           +   AYHG T+  + L G  + +S    L+   +      C         G  E + I  
Sbjct: 169 SLRNAYHGDTVGAVALGGMALFHSIYAPLLFDTVKAESPYCYRCPFGRQAGSCERECITH 228

Query: 188 IERIFKNDAQPQDIAAIIIEP-VQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGA 246
           +E +F       ++ A ++EP VQG  G  +    +++R+R LCD+HG+ L+ADEV  G 
Sbjct: 229 METLFARHGH--ELCAAVVEPLVQGAAGMLLQPPGWLRRVRELCDEHGVFLVADEVAVGF 286

Query: 247 GRTGTFFATEQLGIVPDLTTFAKSVGGGF-PISGVAGKAEIMDA-------IAPGGLGGT 298
           G+TGT FA EQ G+ PD    AK + GG+ P++       + D        +     G T
Sbjct: 287 GKTGTLFACEQEGVTPDFLCLAKGISGGYLPLAATLTTERVHDGFLARHEELRTFFHGHT 346

Query: 299 YAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAI 358
           Y G+P+ACAAA+A L VFEEE+++ER Q    RL A L  ++    V GD+R  G M  I
Sbjct: 347 YTGNPLACAAAIASLDVFEEERVMERLQPKIARLAARLDTLRDLPHV-GDIRQRGVMTGI 405

Query: 359 ELFEGGDTHKP---AAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLE 412
           E+     T +    A  +  ++ + AR +G+I+   G   +V+  + P++I D +++
Sbjct: 406 EMVRNRATKEAYDLALRVGHRVTLEARRRGVIIRPLG---DVMVLMPPLSITDDEID 459


Lambda     K      H
   0.319    0.137    0.393 

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: 503
Number of extensions: 26
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: 426
Length of database: 491
Length adjustment: 33
Effective length of query: 393
Effective length of database: 458
Effective search space:   179994
Effective search space used:   179994
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: 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