GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Sphingomonas indica Dd16

Align Kynurenine--oxoglutarate transaminase 1; Kynurenine--oxoglutarate transaminase I; Cysteine-S-conjugate beta-lyase; Glutamine transaminase K; GTK; Glutamine--phenylpyruvate transaminase; Kynurenine aminotransferase 1; Kynurenine aminotransferase I; KATI; EC 2.6.1.7; EC 4.4.1.13; EC 2.6.1.64 (characterized)
to candidate WP_085218250.1 B9N75_RS07610 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::Q08415
         (423 letters)



>NCBI__GCF_900177405.1:WP_085218250.1
          Length = 389

 Score =  145 bits (366), Expect = 2e-39
 Identities = 89/254 (35%), Positives = 140/254 (55%), Gaps = 22/254 (8%)

Query: 94  VLVTVGAYGALFTRFQALVDEGDEVIIMEPAFDCYEPMTMMAGGCPVFVTLKPSPAPKGK 153
           +LVT G   A F  F A +D GDEVI++EP +  +     +AGG  V        AP   
Sbjct: 93  ILVTNGLTHASFAAFMAAIDPGDEVILLEPYYPQHVAKVELAGGTVV-------TAP--- 142

Query: 154 LGASNDWQLDPAELASKFTPRTKILVLNTPNNPLGKVFSRMELELVANLCQQHDVVCISD 213
           L A+N++ +  A +A+K TP+T+++VL  P NP G+V++R ELE+VA L   HD++ + D
Sbjct: 143 LDAANNFAISHAAIAAKITPKTRMIVLVNPANPTGRVYTRAELEIVAELAIAHDLIVLCD 202

Query: 214 EVYQWLVYDGHQHVSIASLPGMWDRTLTIGSAGKSFSATGWKVGWVMGPDNIMKHLRTVH 273
           EVY+++ YDG +HVSIASLPGM +RT+T  +  K++S  GW+VG++     ++  +  + 
Sbjct: 203 EVYEYITYDGAEHVSIASLPGMRERTITCFAFTKAYSMDGWRVGYLTADARLIPAILRII 262

Query: 274 QNSIFHCP--TQAQAAVAQCFEREQQHFGQPSSYFLQLPQAMELNRDHMIRSL-QSVGLK 330
              + H     Q  A  A    +E  H          + +A    R+ ++R+L Q  G+ 
Sbjct: 263 TTDVTHVNVFVQEGARAAVTGPQEPMH---------AMVEADRRKREIVVRALNQMPGVT 313

Query: 331 LWISQGSYFLIADI 344
               QG+ +   DI
Sbjct: 314 CAEPQGTIYAFPDI 327


Lambda     K      H
   0.322    0.137    0.431 

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: 384
Number of extensions: 12
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: 423
Length of database: 389
Length adjustment: 31
Effective length of query: 392
Effective length of database: 358
Effective search space:   140336
Effective search space used:   140336
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.

Links

Downloads

Related tools

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