GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Echinicola vietnamensis KMM 6221, DSM 17526

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate Echvi_0577 Echvi_0577 ornithine aminotransferase

Query= curated2:Q8R7C1
         (393 letters)



>FitnessBrowser__Cola:Echvi_0577
          Length = 413

 Score =  272 bits (696), Expect = 1e-77
 Identities = 149/401 (37%), Positives = 223/401 (55%), Gaps = 10/401 (2%)

Query: 2   ITYEKKYLMDTYNRYPIMLVKGEGTRVWDSEGNAYLDFVAGIAVNSLGHCHPALVEAIKK 61
           I  E K+    Y+  P++L +GEG  +WD EG  Y DF++  +  + GHCHP +++ +  
Sbjct: 12  IELENKHGAHNYHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPRILQTLID 71

Query: 62  QAETLIHCSNLYWNEKQIELARMISENSFGGKVFFANSGAEANEGAIKLARKYASLKYG- 120
           QA TL   S  + N+      + ++E     KV   N+GAE  E AIK+ARK+   K G 
Sbjct: 72  QAGTLTLTSRAFHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKIARKWGYEKKGI 131

Query: 121 -GKRYKIITAKNSFHGRTFGALTATGQEKYHKGFGPLLAGFKYVPLNDIEALYEAVDD-- 177
                 II AKN+FHGRT   ++ +  E   K FGP   GF  +P +DI+AL + +    
Sbjct: 132 PENEGTIIVAKNNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDIDALKDVLSQSK 191

Query: 178 EVCAIMLEVIQGEGGIHEATPEYVKAVRKICDENDLLFILDEVQTGIGRTGKLFGYEHYG 237
            +   ++E IQGE G++     Y+K V  +C ++ +LF+ DE+QTGI RTGKL   +H G
Sbjct: 192 NIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIARTGKLLACDHEG 251

Query: 238 VVPDIMTLAKGLGGGF-PIGAIVAKED-KAVFKPGDHASTFGGNPLACAAGIAVLNEVTK 295
           V PD++ L K + GGF P+ A++A +    V +PG H STFGGNPL     +  LN V  
Sbjct: 252 VKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAKVAMTALNVVKD 311

Query: 296 DGFLEGVDKKGKYFREGLETLQKKHKVVKEIRGKGLM----VGCEVDLEDASEIVLKALE 351
           +   E  DK GK FRE ++ L  K  +V+ +RGKGL+    +    D + A  + L   E
Sbjct: 312 EKLAENADKLGKLFRERIQQLVDKSDLVELVRGKGLLNAIVINDTEDSDTAWRLCLALKE 371

Query: 352 KGLLINSVSHNVLRFVPPLIVTEEEIDEALQILDDVLSEIR 392
            GLL      N++RF PPL++TEE++ +   I++  +   +
Sbjct: 372 NGLLAKPTHGNIIRFAPPLVITEEQLHDCCDIIEKTIQNFK 412


Lambda     K      H
   0.319    0.139    0.405 

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: 495
Number of extensions: 25
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: 393
Length of database: 413
Length adjustment: 31
Effective length of query: 362
Effective length of database: 382
Effective search space:   138284
Effective search space used:   138284
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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