GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas stutzeri RCH2

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF2666 Psest_2719 acetylornithine and succinylornithine aminotransferases/succinylornithine transaminase family

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__psRCH2:GFF2666
          Length = 406

 Score =  210 bits (534), Expect = 7e-59
 Identities = 142/401 (35%), Positives = 203/401 (50%), Gaps = 46/401 (11%)

Query: 27  VAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEP 86
           V  R   S VWD  GRE +DFAGGIAV   GH HP ++AA+ EQ GKL H    +   EP
Sbjct: 27  VPVRGLGSRVWDQSGRELVDFAGGIAVNALGHAHPAMVAALTEQAGKLWHIS-NIYTNEP 85

Query: 87  YIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA------ATGRAGVIAFTGAYH 140
            + LA+++   V   F  +     SG+EA E A K+AR          +  +I+   ++H
Sbjct: 86  ALRLAKKL---VAATFADRAFFCNSGAEANEAAFKLARRYAHDVYGPQKFEIISALNSFH 142

Query: 141 GRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQD 200
           GRT+ T+ + G+   YS G G                       I  I  +  ND +   
Sbjct: 143 GRTLFTVTVGGQS-KYSDGFG---------------------PKIEGITHVPYNDLEALK 180

Query: 201 IA------AIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFA 254
            A      A+++EP+QGE G     +++++  R LC++H  LLI DEVQTG GRTG  FA
Sbjct: 181 AAISDKTCAVVLEPIQGESGILPGEQAYLEGARQLCNEHNALLIFDEVQTGMGRTGELFA 240

Query: 255 TEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLK 314
               GI PD+ T AKS+GGGFPI  +    EI   ++ G  G TY G+P+ACA A AV+ 
Sbjct: 241 YMHYGITPDILTNAKSLGGGFPIGAMLTTNEIAAHLSVGTHGTTYGGNPLACAVAEAVVD 300

Query: 315 VFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELV 374
           +    ++LE  +A  ER KA L +I  ++ V   VRG G ++   L    D  K  A   
Sbjct: 301 IVNTPEVLEGVKAKHERFKARLTQIGERYGVFSLVRGRGLLIGCVL---SDAWKGKA--- 354

Query: 375 SKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGL 415
                 A ++ L++L  G   +V+R    + I  A +++GL
Sbjct: 355 GAFCAAAEKEALMVLQAGP--DVVRLAPSLVIDQADIDEGL 393


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: 402
Number of extensions: 15
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: 406
Length adjustment: 31
Effective length of query: 395
Effective length of database: 375
Effective search space:   148125
Effective search space used:   148125
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: 50 (23.9 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