GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Sphingomonas indica Dd16

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_085217210.1 B9N75_RS01575 aspartate aminotransferase family protein

Query= reanno::azobra:AZOBR_RS19025
         (389 letters)



>NCBI__GCF_900177405.1:WP_085217210.1
          Length = 396

 Score =  410 bits (1054), Expect = e-119
 Identities = 207/383 (54%), Positives = 268/383 (69%)

Query: 5   VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64
           +MP Y R+ +   RGEG YLY   G  +LDFA+G+AVN+LGH +P+L +A+  QA  L H
Sbjct: 6   LMPVYPRSPVRPVRGEGCYLYGEGGETYLDFASGIAVNLLGHGHPHLTKAIQDQAATLIH 65

Query: 65  TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124
            SNL+     E+LA+RL ++TFADTVFFTNSGAEA EC  K  R+YH+  G   +  +IT
Sbjct: 66  VSNLYGSPQGEALAQRLVDSTFADTVFFTNSGAEAVECAIKTARRYHHHHGRPEKHTLIT 125

Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184
           F+ AFHGRTL  +SA  Q KL  GF PLL GF +  F +L+A + A+ D TAG  +EP+Q
Sbjct: 126 FKNAFHGRTLGTISATDQAKLRDGFAPLLPGFTVAEFDNLDAAKAAIDDHTAGFLVEPVQ 185

Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244
           GEGGIR  S EF++GLR + DEH L+L LDE+QCG+ RTGKL+A+E  GI PD++A AKG
Sbjct: 186 GEGGIRPASQEFMKGLRALADEHDLMLVLDEVQCGVARTGKLYAYEHYGIEPDILASAKG 245

Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304
           IGGGFP+GACLATEKAA+GM  GTHGSTYGG PLA A G AVLD V  P FL+ V R+G 
Sbjct: 246 IGGGFPMGACLATEKAAAGMVIGTHGSTYGGGPLAMAAGGAVLDVVNTPEFLERVTRMGD 305

Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLL 364
            L+  L  ++  +  +F+ VRG GLMLG+         V  LR +GLL+V AGDNV+R+L
Sbjct: 306 RLRGALEQMIPNHDHLFESVRGLGLMLGIKMKTDSRAFVTYLRDHGLLTVAAGDNVMRVL 365

Query: 365 PPLNIGEAEVEEAVAILAKTAKE 387
           PPL I ++ + E V  L++ A++
Sbjct: 366 PPLVIEDSHIAEFVEKLSEAARQ 388


Lambda     K      H
   0.321    0.139    0.414 

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: 496
Number of extensions: 16
Number of successful extensions: 1
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: 389
Length of database: 396
Length adjustment: 31
Effective length of query: 358
Effective length of database: 365
Effective search space:   130670
Effective search space used:   130670
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