GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Xenophilus azovorans DSM 13620

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_038217041.1 Q392_RS28935 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::Q08415
         (423 letters)



>NCBI__GCF_000745855.1:WP_038217041.1
          Length = 386

 Score =  234 bits (597), Expect = 3e-66
 Identities = 147/410 (35%), Positives = 206/410 (50%), Gaps = 37/410 (9%)

Query: 9   RLDGIDQNLWVEFGKLTKEYDVVNLGQGFPDFSPPDFATQAFQQATSGNFMLNQYTRAFG 68
           RL  +   ++     L  E + VNLGQGFPDF      TQA   A +     NQY    G
Sbjct: 12  RLPSVGTTIFTVMSALAAEKNAVNLGQGFPDFGCDPKLTQAVTDAMAAGH--NQYPPMPG 69

Query: 69  YPPLTNVLASFFGKLLGQEMDPLTNVLVTVGAYGALFTRFQALVDEGDEVIIMEPAFDCY 128
            P L   +A+    L G+  DP T + VT GA  A+ T   ALV  GDEVI++EP +D Y
Sbjct: 70  VPALREAIAAKIEALYGRRYDPATEITVTAGATQAIITTVLALVRPGDEVIVLEPCYDSY 129

Query: 129 EPMTMMAGGCPVFVTLKPSPAPKGKLGASNDWQLDPAELASKFTPRTKILVLNTPNNPLG 188
            P   +AG   V V L P             ++ D   +A+  TPRT+++++NTP+NP  
Sbjct: 130 VPNIELAGAAVVRVPLTPG-----------SFRPDFDRIAAALTPRTRMILINTPHNPSA 178

Query: 189 KVFSRMELELVANLCQQHDVVCISDEVYQWLVYDGHQHVSIASLPGMWDRTLTIGSAGKS 248
            V++  E+  +  L    DV  ISDEVY+ +VYDG +H S+A  PG+  R++ + S GK+
Sbjct: 179 TVWTEGEMRRLEELLAPTDVFVISDEVYEHMVYDGARHESVARFPGLAARSVIVSSFGKT 238

Query: 249 FSATGWKVGWVMGPDNIMKHLRTVHQNSIFHCPTQAQAAVAQCFEREQQHFGQPSSYFLQ 308
           +  TGWKVG+V  P  +    R VHQ ++F   T  Q A+A        +   P+ Y L+
Sbjct: 239 YHVTGWKVGYVAAPAPLTAEFRKVHQFNVFTVNTPMQHALA-------AYMADPAPY-LE 290

Query: 309 LPQAMELNRDHMIRSLQSVGLKLWISQGSYFLIADISDFKSKMPDLPGAEDEPYDRRFAK 368
           LP      RD     L    LKL  SQGSYF   DIS           A  + ++  F +
Sbjct: 291 LPAFYSAKRDLFAEGLARTRLKLLPSQGSYFQCVDIS-----------AVSDLHEAEFCQ 339

Query: 369 WMIKNMGLVGIPVSTFFSRPHQKDFD-HYIRFCFVKDKATLQAMDERLRK 417
           W+   +G+  IP+S F+       FD   +RFC+ K   TL+A  ERL +
Sbjct: 340 WLTAEIGVAAIPLSAFYG----DGFDQRVVRFCYAKKDETLRAALERLAR 385


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: 478
Number of extensions: 22
Number of successful extensions: 6
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: 386
Length adjustment: 31
Effective length of query: 392
Effective length of database: 355
Effective search space:   139160
Effective search space used:   139160
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 25 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