GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cola:Echvi_0150
          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.

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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