GapMind for catabolism of small carbon sources

 

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

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate Echvi_2919 Echvi_2919 Ornithine/acetylornithine aminotransferase

Query= SwissProt::P38021
         (401 letters)



>lcl|FitnessBrowser__Cola:Echvi_2919 Echvi_2919
           Ornithine/acetylornithine aminotransferase
          Length = 393

 Score =  219 bits (557), Expect = 1e-61
 Identities = 138/382 (36%), Positives = 215/382 (56%), Gaps = 32/382 (8%)

Query: 24  PLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKDQADK---ITLTSR 80
           PL I I +A G ++  P+G +Y+D++S     N GHRHPK+++A++DQ DK   + +   
Sbjct: 18  PLLIEIEKAEGIYMYGPKGEKYIDLISGIGVSNVGHRHPKVLKAIQDQLDKYMHLMVYGE 77

Query: 81  AFHNDQLGPFYEKTAKLTGK-EMILPMNTGAEAVESAVKAARRWAYEVKGVADNQAEIIA 139
              + Q       T  L  K + +  +N+G+EAVE A+K A+R+          + EI++
Sbjct: 78  YVQSPQTQLAKALTDTLPKKLDNVYLVNSGSEAVEGALKLAKRYT--------GRREILS 129

Query: 140 CVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITPNTAAFLFEPIQ 199
           CV  +HG +  A+S+   E +KR + P+LPGI+ + + + + L Q IT  TAA + E +Q
Sbjct: 130 CVNAYHGSSHGALSVGGNEIFKRAYRPLLPGIRHLDFNEPDQLDQ-ITEETAAIMVETVQ 188

Query: 200 GEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIVPDMYILGKA 259
           GEAGI +  + + +     C E   L I DEIQ G GRTGK +A     IVPD+ +  K 
Sbjct: 189 GEAGIRVGTKEYFKALRHRCDETGTLLILDEIQAGFGRTGKFWAFQHYDIVPDIVVCAKG 248

Query: 260 LGGGVFPISCIAADREILGVF--NP-GSHGSTFGGNPLACAVSIASLEVLEDEKLADRSL 316
           +GGG+ PI    A + I+ VF  NP   H +TFGG+P++CA ++A++++L DEKL     
Sbjct: 249 MGGGM-PIGAFIAPQSIMSVFKNNPLLGHITTFGGHPVSCAAALATIDILRDEKLIQHVE 307

Query: 317 ELGEYFKSELESIDSPVIKEVRGRGLFIGV--ELTEAARPYCERLKEEG------LLCKE 368
                FK  L   + P I+E+R +GL + V  E  E  +P  +R  E G      L C++
Sbjct: 308 RKANLFKKHL---NHPKIQEIRNKGLMMAVKFEAFEVLKPIIDRAIELGIITDWFLFCED 364

Query: 369 THDTVIRFAPPLIISKEDLDWA 390
           +    +R APPL I+ E+++ A
Sbjct: 365 S----MRIAPPLTITDEEIEKA 382


Lambda     K      H
   0.318    0.136    0.401 

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: 414
Number of extensions: 34
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: 401
Length of database: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
Effective search space:   133940
Effective search space used:   133940
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 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