GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapX in Magnetospirillum magneticum AMB-1

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_011382998.1 AMB_RS02875 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::P16524
         (393 letters)



>lcl|NCBI__GCF_000009985.1:WP_011382998.1 AMB_RS02875 pyridoxal
           phosphate-dependent aminotransferase
          Length = 400

 Score =  227 bits (579), Expect = 4e-64
 Identities = 145/383 (37%), Positives = 216/383 (56%), Gaps = 22/383 (5%)

Query: 14  ISGIRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQA 73
           I+  +K + L A   DVI L  G+PDF TP ++KAAAK AID+ +T Y P AG ++LRQA
Sbjct: 17  IAVTQKAAELKAAGRDVIGLGAGEPDFDTPDNIKAAAKAAIDKGLTKYGPPAGTVDLRQA 76

Query: 74  VQLYMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLC 133
           +    K++   +Y A+ ++ +  G    I  AF   ++PGDEVI+P P +  Y  I  + 
Sbjct: 77  IAAKFKRENGLDYTAD-QVTVGVGGKGVIFNAFMATINPGDEVIVPAPYWVSYPDIALMF 135

Query: 134 GAKPVIVD-TTSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLK 191
           G KPV V    + GFKL    +E A+TP TK +VL  PSNPTG   S +E+K++   LL+
Sbjct: 136 GGKPVFVPCPETAGFKLQPADLEKAITPRTKWLVLNSPSNPTGAAYSWDEMKALTDVLLR 195

Query: 192 GRNVFVLSDEIYSELTYDRPHY----SIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPK 247
             +V+++SD++Y  L YD   +     +   L D+T+ +NG+SK+++MTGWR+G+   P 
Sbjct: 196 HPHVWIMSDDMYEHLVYDDFKFCTPAQVEPKLYDRTLTMNGVSKAYAMTGWRVGYAAGPA 255

Query: 248 DIAKHILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQ-YKKRLDYVYDRLVSM-G 305
            I K I  +   +V+  SSISQ A++EA+ NG  D +      +K+R D +   L    G
Sbjct: 256 AIIKAINMIQSQSVTHTSSISQAASVEAL-NGTQDFIPKNAAVFKRRRDLIVGLLNQCPG 314

Query: 306 LDVVKPSGAFYIFPSIK----------SFGMTSFDFSMALLEDAGVALVPGSSFSTYGEG 355
           +    P GAFY++PS                   DF  ALLE  GVA+V G++F    E 
Sbjct: 315 ITCRTPEGAFYVYPSCAGVIGKKTPDGKVIANDTDFVGALLEAEGVAVVQGAAFGL--EP 372

Query: 356 YVRLSFACSMDTLREGLDRLELF 378
           Y R+S+A S   L +  +R++ F
Sbjct: 373 YFRISYATSDAALTKAAERIKRF 395


Lambda     K      H
   0.319    0.135    0.388 

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: 353
Number of extensions: 23
Number of successful extensions: 8
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: 393
Length of database: 400
Length adjustment: 31
Effective length of query: 362
Effective length of database: 369
Effective search space:   133578
Effective search space used:   133578
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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