GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Paucidesulfovibrio gracilis DSM 16080

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_078718069.1 B5D49_RS12615 ornithine--oxo-acid transaminase

Query= curated2:O27392
         (390 letters)



>NCBI__GCF_900167125.1:WP_078718069.1
          Length = 399

 Score =  300 bits (767), Expect = 6e-86
 Identities = 164/400 (41%), Positives = 236/400 (59%), Gaps = 14/400 (3%)

Query: 1   MDSEEIIELERKFIMQTYTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKV 60
           M  ++ I+LE ++  Q Y    +VLS G+G  VWD+E N Y+DC +  +  + GH HP++
Sbjct: 1   MKPQDYIDLENRYGAQNYKPLDVVLSKGEGVWVWDVEDNRYMDCLSAYSAVNQGHCHPRI 60

Query: 61  ALAICHQAQRLIHSSNIYYTREQVELAKLLTAISPHDRVFFANSGAEANEGAIKLARKF- 119
             A+  QA+RL  +S  +   +   L + L  ++   +V   NSGAEA E AIK  RK+ 
Sbjct: 61  VAALQEQAERLPLTSRAFRNDQLGLLYEELCRLTNSHKVLPMNSGAEAVETAIKAVRKWG 120

Query: 120 -------TGKSEIIAAENSFHGRTLATVTATGQKKYSEPFRPLPEGFKHVPYGDIGAMAD 172
                    ++EII   N+FHGRT++ V+ +        F P   GF+ +P+GD  A   
Sbjct: 121 YMEKGVPENQAEIIVCANNFHGRTISIVSFSTDSGARAGFGPFTPGFRVIPFGDAQAFEQ 180

Query: 173 AVGDETAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGRTGAMFAS 232
           A+   T A+++EP+QGE GVIIPPEGYL+ V+EL   + + LILDE+QTG GRTG + A 
Sbjct: 181 AITPHTVALLVEPIQGEAGVIIPPEGYLRRVRELCDTHGIQLILDEIQTGLGRTGKLLAE 240

Query: 233 QLFGVEPDITTVAKAMGGG-YPIGAVLANERVAMAFEPGDHGSTFGGNPWGCAAAIATIE 291
           +  G+E DIT + KA+ GG YP+ AVL+N  V     PG+HGSTFGGNP  CA A A + 
Sbjct: 241 EHEGIEADITLIGKALSGGLYPVSAVLSNTEVLGILRPGEHGSTFGGNPLACAVARAALN 300

Query: 292 VLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEIDGECAGV---VDAA 348
           VL++E L   A  MG  F+  LR + +   AVRD+RG GL++ +E+D    G     +  
Sbjct: 301 VLVEEGLIANAELMGQRFMKGLRAIAN--PAVRDVRGRGLLLAVELDPSAGGARPYCERL 358

Query: 349 REMGVLINCTAGKVIRIVPPLVIKKEEIDAAVDVLGHVIS 388
           +E G+L   T    IR  PPLVI  E++D A++ +  V+S
Sbjct: 359 KEAGLLCKETHENTIRFAPPLVITAEQVDWALERISSVLS 398


Lambda     K      H
   0.320    0.138    0.404 

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: 398
Number of extensions: 16
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: 390
Length of database: 399
Length adjustment: 31
Effective length of query: 359
Effective length of database: 368
Effective search space:   132112
Effective search space used:   132112
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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