GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Klebsiella michiganensis M5al

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate BWI76_RS07600 BWI76_RS07600 aspartate aminotransferase family protein

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__Koxy:BWI76_RS07600
          Length = 445

 Score =  218 bits (555), Expect = 3e-61
 Identities = 154/422 (36%), Positives = 226/422 (53%), Gaps = 28/422 (6%)

Query: 21  GQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQ 80
           G +HP+V   A+   +WD EG  Y+DF+  +  +N G+ HP+V+AA++ QL  L  T   
Sbjct: 32  GNLHPLVIAGAKGCELWDYEGNTYLDFSSQLVNVNIGYQHPRVLAAMKAQLEALV-TIAP 90

Query: 81  VLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATGRAGVIAFTGAYH 140
             A     E A+ I +  P  F  K     +G++A ENA+++AR  TGR  V++   +YH
Sbjct: 91  ATANLARGEAAKRIVELAPEGF-SKVFFTNAGADANENAIRMARLYTGRDKVLSAYRSYH 149

Query: 141 GRTMMTLGLTG--KVVP--YSAG-MGLMPGGIFRALAPCELHGVSEDD----SIASIERI 191
           G T   +  TG  + VP  YS G +      ++R+    E +  +E++    ++A + R+
Sbjct: 150 GNTGSAIAATGDWRRVPNEYSRGHVHFFNPYLYRS----EFNATTEEEECQRALAHLRRM 205

Query: 192 FKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGT 251
            + +  P  IAAI++E + G  G  V  + +MQ +RAL D+ GI+LI DEV  G GRTG+
Sbjct: 206 IECEG-PNAIAAILLESIPGTAGILVPPEGYMQGVRALADEFGIILILDEVMAGFGRTGS 264

Query: 252 FFATEQLGIVPDLTTFAKSVGGGF-PISGVAGKAEIM----DAIAPGGLGGTYAGSPIAC 306
           +FA EQ G+VPDL TFAK V  G+ P  GV     I     D    GGL  TY+G P+A 
Sbjct: 265 WFAFEQDGVVPDLVTFAKGVNAGYVPAGGVLISEPIARYFDDHFFAGGL--TYSGHPLAM 322

Query: 307 AAALAVLKVFEEEKLLERSQAVG-ERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGD 365
           AA +A +   +EEK++E +  +G E L+ GL  +  KH +IG+VRG G   A+EL    +
Sbjct: 323 AAIVATIDAMKEEKVVENAATIGNEVLRPGLEALAEKHAIIGNVRGRGLFQALELVSSRE 382

Query: 366 THKP-AAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDE 424
              P  A  ++ I     E GL+        N I  + P TI   Q+ KGLAI    F  
Sbjct: 383 HKTPLGAADMAAIKGALTEAGLLAF---VVENRIHVVPPCTISAEQVAKGLAIFDAVFAR 439

Query: 425 LA 426
            A
Sbjct: 440 FA 441


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: 445
Number of extensions: 22
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: 426
Length of database: 445
Length adjustment: 32
Effective length of query: 394
Effective length of database: 413
Effective search space:   162722
Effective search space used:   162722
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