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_085217296.1 B9N75_RS02070 aminotransferase

Query= SwissProt::Q08415
         (423 letters)



>NCBI__GCF_900177405.1:WP_085217296.1
          Length = 384

 Score =  219 bits (559), Expect = 9e-62
 Identities = 133/393 (33%), Positives = 199/393 (50%), Gaps = 39/393 (9%)

Query: 26  KEYDVVNLGQGFPDFS-PPDFATQAFQQATSGNFMLNQYTRAFGYPPLTNVLASFFGKLL 84
           +E   VNLGQGFPDF  P D   +A +  T      +QY    G P L   +A  + +  
Sbjct: 21  RELGAVNLGQGFPDFGWPEDVVAKAAELLTGA---ASQYPPMRGLPELRAAVADHYSQHQ 77

Query: 85  GQEMDPLTNVLVTVGAYGALFTRFQALVDEGDEVIIMEPAFDCYEPMTMMAGGCPVFVTL 144
           G    P   + VT GA  AL +   AL++ GDEV++ +P +D Y PM    GG P +V L
Sbjct: 78  GIAYAP-DEITVTSGATEALASALLALIEPGDEVLLFQPLYDAYVPMVRRGGGVPRYVAL 136

Query: 145 KPSPAPKGKLGASNDWQLDPAELASKFTPRTKILVLNTPNNPLGKVFSRMELELVANLCQ 204
           +P            +W++    + +  TPRT+++V N P+NP G+ FS+ EL  +A +C 
Sbjct: 137 RPP-----------EWRITREAIEAALTPRTRLVVFNNPHNPTGRAFSQDELTALAEVCV 185

Query: 205 QHDVVCISDEVYQWLVYDGHQHVSIASLPGMWDRTLTIGSAGKSFSATGWKVGWVMGPDN 264
             D++ +SDEV++ ++  G  H+ +ASLPGM DRT+ +GSAGK FS TGWKVGW+  P  
Sbjct: 186 ARDLIVLSDEVWEHVMPGGAAHLPLASLPGMSDRTVKVGSAGKIFSLTGWKVGWIAAPAA 245

Query: 265 IMKHLRTVHQNSIFHCPTQAQAAVAQCFEREQQHFGQPSSYFLQLPQAMELNRDHMIRSL 324
           +   +   HQ   F  P   QAAVA          G+  +Y+  +  A  + RD +   L
Sbjct: 246 LGDPITKAHQFVTFTTPPNLQAAVA-------YGLGKDEAYYRDMRAAFAVARDRLADGL 298

Query: 325 QSVGLKLWISQGSYFLIADISDFKSKMPDLPGAEDEPYDRRFAKWMIKNMGLVGIPVSTF 384
              G  +   +GSYFL  D++       DL           F +  ++  G+  IP++ F
Sbjct: 299 ADAGYVVLPGEGSYFLCVDLTASGIAADDL----------TFCERAVREAGIAAIPLTAF 348

Query: 385 FSRPHQKDFDHYIRFCFVKDKATLQAMDERLRK 417
           F    +    + IR CF K + T+   DE L++
Sbjct: 349 F---EETPVTNVIRLCFAKKQETI---DEGLKR 375


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: 455
Number of extensions: 19
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: 423
Length of database: 384
Length adjustment: 31
Effective length of query: 392
Effective length of database: 353
Effective search space:   138376
Effective search space used:   138376
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