GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Phyllobacterium endophyticum PEPV15

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_106714946.1 CU100_RS02400 aspartate aminotransferase family protein

Query= curated2:O27392
         (390 letters)



>NCBI__GCF_003010935.1:WP_106714946.1
          Length = 441

 Score =  187 bits (475), Expect = 5e-52
 Identities = 142/421 (33%), Positives = 208/421 (49%), Gaps = 52/421 (12%)

Query: 18  YTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAICHQAQRLIHSSNI 77
           +   P +L   K       +G   +D  AG+   + GH  P++  A+  Q   L ++   
Sbjct: 24  FKENPRLLVSAKDMHYKSHDGREILDGTAGLWCCNAGHGRPRIVEAVQKQVAELDYAPAF 83

Query: 78  YYTREQV-ELAKLLTAI--SPHDRVFFANSGAEANEGAIKLARKFTG------KSEIIAA 128
                +  ELA  L A+  SP D VFF NSG+E+ + A+K+A  +        K ++I  
Sbjct: 84  QMGHPKAFELAARLAAMLPSPLDHVFFTNSGSESVDTALKIALAYHRAKGNGTKVKLIGR 143

Query: 129 ENSFHGRTLATVTATGQKKYSEPFRPLPEGFKHV----------------PYG------- 165
           E  +HG     ++  G     + F     G  H+                 YG       
Sbjct: 144 ERGYHGVGFGGISVGGISGNRKTFGNALSGIDHIRHTHDLARNAYTRGEPEYGAEFADDL 203

Query: 166 -DIGAMADAVGDETAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFG 224
             + A+ DA     AA+I+EPV G  GV+IPP+GYLK ++E+  ++D+LLI DEV TGFG
Sbjct: 204 EKVVALHDA--SNIAAVIVEPVAGSTGVLIPPKGYLKRLREICTKHDILLIFDEVITGFG 261

Query: 225 RTGAMFASQLFGVEPDITTVAKAMGGG-YPIGAVLANERVAMAFEPGD-------HGSTF 276
           R G  FA   FGV PD+ T AK +  G  P+GAV A++++   F  G        HG T+
Sbjct: 262 RLGTPFAVDYFGVVPDLVTTAKGITSGVIPMGAVFASKQIYETFMTGAENMIELFHGYTY 321

Query: 277 GGNPWGCAAAIATIEVLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIE 336
            G+P  CAAA+AT++   +E L  RA+++  Y+   L   L G   V DIR +GL+  IE
Sbjct: 322 SGHPVACAAALATLDTYEEEGLLTRASEISGYWEEAL-HALKGLPHVIDIRNLGLIGAIE 380

Query: 337 IDG-ECAGVVDA------AREMGVLINCTAGKVIRIVPPLVIKKEEIDAAVDVLGHVISD 389
           ++  E A    A      A E GVLI  T G +I + PPL+I K +I+   D L  V+ +
Sbjct: 381 LEPIEGAPTKRAFQAFLKAYEKGVLIR-TTGDIIALSPPLIISKGQIEHLFDTLADVLKN 439

Query: 390 L 390
           L
Sbjct: 440 L 440


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: 460
Number of extensions: 33
Number of successful extensions: 7
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: 441
Length adjustment: 31
Effective length of query: 359
Effective length of database: 410
Effective search space:   147190
Effective search space used:   147190
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 26 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