GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Sphingomonas indica Dd16

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_085218250.1 B9N75_RS07610 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::P9WPZ5
         (397 letters)



>NCBI__GCF_900177405.1:WP_085218250.1
          Length = 389

 Score =  158 bits (399), Expect = 3e-43
 Identities = 98/308 (31%), Positives = 164/308 (53%), Gaps = 5/308 (1%)

Query: 21  ATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGSAPLRRAIAAQRRRHFGV 80
           A  +  ++L  G P  D P  + +A + A+  G+  Y    G+   R+A+A +      +
Sbjct: 27  AQGLDLIHLEFGRPHADTPGHIKEAVKTALDAGIVHYGDFRGTLSFRQALAEKLTDFNKL 86

Query: 81  DYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVVAMAGAHRVTVPLVP 140
           DY  + E+LVT G T A  AA +  ++PG EV+L+EP+Y  +   V +AG   VT PL  
Sbjct: 87  DYGVD-EILVTNGLTHASFAAFMAAIDPGDEVILLEPYYPQHVAKVELAGGTVVTAPL-D 144

Query: 141 DGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAIAEIAVAANLVVITDEV 200
               FA+   A+   +TP+TR +++ +P NPTG V +  EL  +AE+A+A +L+V+ DEV
Sbjct: 145 AANNFAISHAAIAAKITPKTRMIVLVNPANPTGRVYTRAELEIVAELAIAHDLIVLCDEV 204

Query: 201 YEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWACGPAELIAGV-RAAKQ 259
           YE++ +D A H+ +A   GM ERTIT  +  K ++  GW++G+    A LI  + R    
Sbjct: 205 YEYITYDGAEHVSIASLPGMRERTITCFAFTKAYSMDGWRVGYLTADARLIPAILRIITT 264

Query: 260 YLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTEI-GFAVHDSYGTYFL 318
            +++V     + A A     ++  + A+  + R +R+ +   L ++ G    +  GT + 
Sbjct: 265 DVTHVNVFVQEGARAAVTGPQEP-MHAMVEADRRKREIVVRALNQMPGVTCAEPQGTIYA 323

Query: 319 CADPRPLG 326
             D R  G
Sbjct: 324 FPDIRGTG 331


Lambda     K      H
   0.321    0.135    0.405 

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: 359
Number of extensions: 16
Number of successful extensions: 3
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: 397
Length of database: 389
Length adjustment: 31
Effective length of query: 366
Effective length of database: 358
Effective search space:   131028
Effective search space used:   131028
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 (21.9 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