GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Azospirillum brasilense Sp245

Align 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39) (characterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase

Query= reanno::Smeli:SMc04386
         (410 letters)



>FitnessBrowser__azobra:AZOBR_RS24065
          Length = 392

 Score =  220 bits (561), Expect = 5e-62
 Identities = 136/371 (36%), Positives = 200/371 (53%), Gaps = 18/371 (4%)

Query: 37  KREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAIREKFQRENG 96
           K  G+ VI+L  G+PDFDTP  V+ AA  A+H G+T YT + G PEL+ A+     R  G
Sbjct: 28  KGRGEDVIVLSVGDPDFDTPAPVRDAAIAALHAGDTHYTPIPGRPELRAALARDVARRTG 87

Query: 97  LAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEGKPVLIACDA 156
           L  E + + V  GA+  LFNA +  ++ GDEV++P P + +Y   V       V +A DA
Sbjct: 88  LPVEPENVIVCAGAQNGLFNATLCLVEAGDEVLVPEPMYLTYEACVRASGATLVPVAPDA 147

Query: 157 SSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHPHVWLLVDDM 216
           ++  RL    L AA+TPRTR + L +P+NP+G   SA +   + ++  RH  +W++ D++
Sbjct: 148 AT-LRLDPAALAAAVTPRTRAIFLATPANPTGIVMSAEELEAVADLARRH-DLWVVADEV 205

Query: 217 YEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPRELIKAMAVVQ- 275
           Y  + +D  R        PG+  RT+T+N +SK++AMTGWR G+   P  L+  M  +  
Sbjct: 206 YASLTFD--RPHIGIATLPGMAERTVTINSLSKSHAMTGWRAGWVVAPAPLVAHMGTLAL 263

Query: 276 SQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLDCRVPEGAFY 335
                 P  + QAA VA   G +     R E ++RRRD+ +  L ++ GL C  PE    
Sbjct: 264 CMLYGLPGFVQQAALVAVEQGDEAVAAMR-EGYRRRRDIALEALGSVPGLRCLKPE---- 318

Query: 336 TFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFG--LSPFFRISYATSEA 393
                AG+   V   G  + T  +F   L  +  V+V+   AFG   +   R+S+A SEA
Sbjct: 319 -----AGMFMLVDVRGTGLPT-MEFAWRLFRETGVSVLDAGAFGPAAAGCVRLSFAVSEA 372

Query: 394 ELKEALERIAA 404
           EL EA  RIAA
Sbjct: 373 ELAEACRRIAA 383


Lambda     K      H
   0.318    0.134    0.393 

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: 396
Number of extensions: 23
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: 410
Length of database: 392
Length adjustment: 31
Effective length of query: 379
Effective length of database: 361
Effective search space:   136819
Effective search space used:   136819
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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