GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Echinicola vietnamensis KMM 6221, DSM 17526

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate Echvi_0150 Echvi_0150 glutamate-1-semialdehyde-2,1-aminomutase

Query= SwissProt::Q5JEW1
         (445 letters)



>lcl|FitnessBrowser__Cola:Echvi_0150 Echvi_0150
           glutamate-1-semialdehyde-2,1-aminomutase
          Length = 429

 Score =  139 bits (351), Expect = 1e-37
 Identities = 123/420 (29%), Positives = 188/420 (44%), Gaps = 37/420 (8%)

Query: 37  PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96
           P+ I++ EG  ++D D N + +  +  G + +GH+HP + EAI K  E  T +       
Sbjct: 35  PLFIKKAEGAYLFDEDDNRYIELINSWGPMILGHNHPEINEAIVKAVENGTSFGAPT--- 91

Query: 97  ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156
              I +AE + ++ P     KV   NSG EA  +A++L +  TGR +FL F   +HG   
Sbjct: 92  AKEIDIAELICKMVPS--VEKVRMVNSGTEATMSAVRLARGYTGRDKFLKFEGNYHGHGD 149

Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216
           + L    S  +      P  PGVT              D    P    N V + +E    
Sbjct: 150 SFLIAAGSGAMTMGA--PNSPGVT---------KGTAKDTLLAPYNDLNAVKEVLE---- 194

Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276
                 E+ AI  EP+ G  G V+P +GF + L+K  DE GI+L  DEV  G  R  +  
Sbjct: 195 --ANRDEVAAIILEPVPGNMGLVLPNEGFLQGLRKLCDEEGIVLIFDEVMTGF-RLAQGG 251

Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI----TFDKPGRHATTFGGNPVAIAAGI 332
           A E FGV PDL   GK IGGG+P+     + +I    +   P   A T  GNP+A+AAG 
Sbjct: 252 AQEVFGVTPDLTTMGKIIGGGMPVGAYGGKKEIMDFVSPVGPVYQAGTLSGNPIAMAAGF 311

Query: 333 EVVEIV---KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEK 389
            +++ +    E+   + + G  L   ++   EK  +      LG   ++   K K    +
Sbjct: 312 AMLDHLYQHPEVYQQLDQAGSKLVAGVKSSVEKLGLEYTMTHLGSMYSLFFTKEKVVDFE 371

Query: 390 YPELRDRIV-----KESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEALKAAL 444
             +  D ++     +   KRG+ L      S+     L  T E ID  ++  E +L+  L
Sbjct: 372 TAKTSDTVLFGKYFQAMLKRGVYLPPSQFESLFLSTAL--TDEHIDQIIDANEASLREIL 429


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: 481
Number of extensions: 27
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: 429
Length adjustment: 32
Effective length of query: 413
Effective length of database: 397
Effective search space:   163961
Effective search space used:   163961
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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