GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Desulfoscipio geothermicus DSM 3669

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_207545101.1 BM299_RS02525 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_900115975.1:WP_207545101.1
          Length = 434

 Score =  303 bits (777), Expect = 5e-87
 Identities = 164/434 (37%), Positives = 249/434 (57%), Gaps = 11/434 (2%)

Query: 17  EVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVV 76
           E++ R  + +A    +  +  + +E+ +G  + DV+G  + DF  G+G +N GH    VV
Sbjct: 7   ELVARKHQLIARGISN--STEVFVEKAQGATIVDVEGKEYIDFYGGIGTLNAGHCPAPVV 64

Query: 77  EAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVK 136
           EAIK QAEK  H       YE  + LAEKLIEL PG+ +++V++ NSGAE  E A+K+ +
Sbjct: 65  EAIKNQAEKLLHTCFMVTMYEPYLDLAEKLIELTPGNFDKRVMFVNSGAECVENAVKIAR 124

Query: 137 YGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDG 196
               R   ++F  AFHGRT   +SLT+     + GF P  P V  IP    YR T+    
Sbjct: 125 SYAKRTGIISFECAFHGRTLMTMSLTSKVKPYKFGFGPFAPEVYKIPSAYCYRCTY---- 180

Query: 197 YEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEY 256
                E     L+  +      VPP  I A+  EP+QGEGG++VPP  F   L+K  D++
Sbjct: 181 RSTYPECGLHCLEQFDRMFAAEVPPENIAAMIIEPVQGEGGFIVPPPEFLPGLRKICDKH 240

Query: 257 GILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPG 315
           GI+L  DEVQ G GRTGK +A EHFG+EPDL+   K+I  G+PL+ V+ +ADI     PG
Sbjct: 241 GIILIADEVQTGFGRTGKMFACEHFGLEPDLMTMAKSIAAGMPLSAVVGKADIMNAPNPG 300

Query: 316 RHATTFGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLG 373
               T+ GNPV+ AAG+  ++ +++  L+     +GD   + +   +EKY +IGD RGLG
Sbjct: 301 EIGGTYSGNPVSCAAGLATIDFMQQQNLVERANVIGDKTKQRMLAMQEKYPIIGDVRGLG 360

Query: 374 LAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDV 431
              A+E+VK + TKE   E    ++K     G++++G G   N +R + PL++T E+++ 
Sbjct: 361 AMNAMELVKDRNTKEPAKEETAAVIKHCVDNGVIVIGAGIFSNVVRTLIPLVITDEQLEK 420

Query: 432 AMEIFEEALKAALK 445
            +++ E+A+ +  K
Sbjct: 421 GLDVLEQAVASVSK 434


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: 512
Number of extensions: 27
Number of successful extensions: 5
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: 434
Length adjustment: 32
Effective length of query: 413
Effective length of database: 402
Effective search space:   166026
Effective search space used:   166026
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 Apr 09 2024. 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