GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Azospirillum brasilense Sp245

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate AZOBR_RS19590 AZOBR_RS19590 ornithine-oxoacid aminotransferase

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__azobra:AZOBR_RS19590
          Length = 405

 Score =  253 bits (646), Expect = 7e-72
 Identities = 149/394 (37%), Positives = 212/394 (53%), Gaps = 13/394 (3%)

Query: 12  LLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVK 71
           L+  E  L +  Y   D+++ RG+G  VWD EGN Y+DC+  Y   N GH +P+++EA+ 
Sbjct: 8   LIGTEHRLGAHNYKPLDVVLARGEGVYVWDTEGNRYLDCLSAYSAVNQGHCHPKILEAMV 67

Query: 72  RQAETLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFAR------ 125
           +QA  L    +         FY  L A+     +++ P+NSG EA E+A+K  R      
Sbjct: 68  QQASKLTLTSRAFRNDQLALFYEELAALTGS--HKILPMNSGAEAVESAIKTVRKWGYEV 125

Query: 126 --AHTGRKKFVAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVD 183
                 + + +     F GRT+  +S + +P  R  F P       +P+ D  AL+ A+ 
Sbjct: 126 RGVPENQAEIIVCSDNFHGRTISIVSFSTDPDARGGFGPFTPGFRTVPFGDAAALEAALT 185

Query: 184 EETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHF 243
             T AV+LEP+QGE GV      +LR  R++  E+  ++ILDEIQTG+GRTGK  A EH 
Sbjct: 186 PNTVAVLLEPIQGEAGVVIPPAGYLRRVRDLCTERNVVMILDEIQTGLGRTGKLLAEEHE 245

Query: 244 GIVPDILTLAKALGGG-VPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLE 302
           G+  D+  + KAL GG  P+ A +   EV   +  G HG+TFGGNPLA A   AA+R L 
Sbjct: 246 GVEADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAVARAAMRVLV 305

Query: 303 RTRLWERAAELGPWFMEKLRAIPSPKIREVRGMGLMVGLELKEKA--APYIARLEKEHRV 360
              + + AA  G +F+E+L AI S  IRE RG GLM+ +EL  +A  A       +   V
Sbjct: 306 EEGMIDNAAAQGAYFLEQLGAIRSNVIREARGRGLMLAVELHPEAGGARRYCEALRARGV 365

Query: 361 LALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVL 394
           LA       IR  PPLVI +E ++  +E   AVL
Sbjct: 366 LAKDTHDHTIRIAPPLVITREQVDWALEQFDAVL 399


Lambda     K      H
   0.319    0.137    0.402 

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: 364
Number of extensions: 17
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: 395
Length of database: 405
Length adjustment: 31
Effective length of query: 364
Effective length of database: 374
Effective search space:   136136
Effective search space used:   136136
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