GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Collimonas arenae Ter10

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_128083232.1 CAter10_RS21330 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_001584165.1:WP_128083232.1
          Length = 420

 Score =  263 bits (671), Expect = 1e-74
 Identities = 150/399 (37%), Positives = 225/399 (56%), Gaps = 17/399 (4%)

Query: 48  VYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLI 107
           ++DV+G  F DFA+G+ V+N GH HP++V AI++Q  KFTH +     Y + + LAE++ 
Sbjct: 29  IWDVEGRRFIDFAAGIAVLNTGHRHPKLVAAIQEQLGKFTHTAYQIVPYGSYVELAERIN 88

Query: 108 ELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWV 167
            + PGD  +K  + ++GAEA E A+K+ +  TGR   +AF  AFHGRT   ++LT     
Sbjct: 89  AVTPGDHAKKTTFFSTGAEAVENAVKIARAATGRSAVIAFSGAFHGRTMMGMALTGKVVP 148

Query: 168 QQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAI 227
            + GF P    V H+P+P            E         L  ++      V P  + AI
Sbjct: 149 YKVGFGPFPAEVYHVPFP-----------VELHGVSIENSLAALQSLFKADVDPKRVAAI 197

Query: 228 FFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDL 287
             EP+QGEGG+   P  F +AL+K  DE+GILL  DEVQ G  RTGK +A+EH GV PDL
Sbjct: 198 ILEPVQGEGGFYAAPPAFMQALRKLCDEHGILLVVDEVQTGFARTGKLFAVEHSGVIPDL 257

Query: 288 IQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIVKE--LLPH 344
           +   K++ GG+PL+ V  RA+I     PG    T+ GNP+A+A+ + V+++++E  L+  
Sbjct: 258 MTMAKSLAGGMPLSAVCGRAEIMDAAAPGGLGGTYAGNPLAVASALAVLDVIEEEKLVER 317

Query: 345 VQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRIVKESAKR 404
              +G  L + LE  +     I D RGLG   AVE  +   +K+   +   ++  E+ K 
Sbjct: 318 ANVLGGRLKQVLEGLRADVPQIADIRGLGAMVAVEFTQ-PGSKQPDADFTKKVQAEALKN 376

Query: 405 GLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALK 441
           GL+LL CG   N+IRF+ PL +    +D A+ I  +A++
Sbjct: 377 GLLLLSCGVYSNAIRFLFPLTIEDALMDEALAILSKAMR 415


Lambda     K      H
   0.320    0.141    0.418 

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: 487
Number of extensions: 25
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: 445
Length of database: 420
Length adjustment: 32
Effective length of query: 413
Effective length of database: 388
Effective search space:   160244
Effective search space used:   160244
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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