GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Azospirillum brasilense Sp245

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate AZOBR_RS19025 AZOBR_RS19025 acetylornithine aminotransferase

Query= reanno::WCS417:GFF4238
         (406 letters)



>FitnessBrowser__azobra:AZOBR_RS19025
          Length = 389

 Score =  324 bits (830), Expect = 3e-93
 Identities = 174/389 (44%), Positives = 236/389 (60%), Gaps = 5/389 (1%)

Query: 16  VMVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLW 75
           V++P YA A  +  RGEG  ++   GR  +DFA G+AVNVLGHA+P LV ALT QAHKLW
Sbjct: 4   VVMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLW 63

Query: 76  HVSNVFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFDRFGSEKYEII 135
           H SN+F       LA +L +ATFA+ VFF NSGAEA E   KL R+  +++    +  II
Sbjct: 64  HTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRII 123

Query: 136 AALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKAAVSDKTCAVVLEPI 195
               +FHGRTL  V+   Q K   GFGP + G   VP+ DL+A++ AV+D+T  + LEPI
Sbjct: 124 TFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPI 183

Query: 196 QGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYGVTPDILTSAK 255
           QGEGG+    + +L+G R++CD +  LL  DE+Q GMGR+G LFA++  G+TPD++  AK
Sbjct: 184 QGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAK 243

Query: 256 SLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLAGVNAKH 315
            +GGGFP+ A L TE  A  +  GTHG+TYGGNPLA AV  AV+D +  P  L  V    
Sbjct: 244 GIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIG 303

Query: 316 DLFKARLE-QIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNAAEKENLMILQAGPD 374
            L + RL   + +   +F  VRG GL+LG     A      DV  A     L+ + AG +
Sbjct: 304 GLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPA----VGDVVVALRANGLLSVPAGDN 359

Query: 375 VVRFAPSLVVEDADIKEGLDRFERAVKAL 403
           VVR  P L + +A+++E +    +  K L
Sbjct: 360 VVRLLPPLNIGEAEVEEAVAILAKTAKEL 388


Lambda     K      H
   0.320    0.137    0.400 

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: 418
Number of extensions: 7
Number of successful extensions: 2
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: 406
Length of database: 389
Length adjustment: 31
Effective length of query: 375
Effective length of database: 358
Effective search space:   134250
Effective search space used:   134250
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 Apr 09 2024. The underlying query database was built on Apr 09 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