GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Sinorhizobium meliloti 1021

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate SMc02413 SMc02413 aminotransferase

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__Smeli:SMc02413
          Length = 437

 Score =  241 bits (614), Expect = 4e-68
 Identities = 140/390 (35%), Positives = 213/390 (54%), Gaps = 7/390 (1%)

Query: 40  EGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVP 99
           +GR+ +DF+      + GH HP +  AV   L   +   +   A E  + LAE++   VP
Sbjct: 37  DGRQLLDFSASWGAASLGHSHPAIREAVGRALSDQAGASYLSSANEACVLLAEKLLSLVP 96

Query: 100 GDFPKKTLLVTSGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSA- 158
                +     SGS+A E   +I  AATGR  ++AF GAYHG T+ ++G++G      + 
Sbjct: 97  ERARGRVWFGHSGSDANETVARIVVAATGRPRILAFHGAYHGGTIGSMGVSGHPAQQGSR 156

Query: 159 --GMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFY 216
             G+ L+P     A    E    + D ++A +ER+F  +  P+++AA  IEP+Q +GG  
Sbjct: 157 AEGLTLVPYPNSYAAGSPE---AARDAALAHLERLFATEVPPEEVAAFFIEPIQSDGGML 213

Query: 217 VNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFP 276
           V    F + + ALC +HGIL+++DEV+ G GR+G F A E  GI PD+  F K +GGG P
Sbjct: 214 VPPDGFFKAVEALCRRHGILIVSDEVKVGLGRSGRFNAFEHSGIEPDIVVFGKGLGGGLP 273

Query: 277 ISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGL 336
           IS V G   IM+      L  T  G+P+  AAALAVL+  E + L+  +   G+ L+  L
Sbjct: 274 ISAVVGPEAIMNHSVAFSL-QTVHGNPVCAAAALAVLQTIERDHLILNADRSGKVLREAL 332

Query: 337 REIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRAREKGLILLSCGTYYN 396
             + A+H +IGDVRG G  + IEL     + +PA+   +  V RA + GL+L   G   N
Sbjct: 333 DRLTARHTLIGDVRGRGLALGIELVTDPASREPASRQAALTVYRAFQLGLVLYYVGVQSN 392

Query: 397 VIRFLMPVTIPDAQLEKGLAILAECFDELA 426
           V+    P+T+  A+ E G+A+L +   ++A
Sbjct: 393 VLELTPPLTLTPAEAESGVAMLGQALADVA 422


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: 482
Number of extensions: 24
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: 437
Length adjustment: 32
Effective length of query: 394
Effective length of database: 405
Effective search space:   159570
Effective search space used:   159570
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