GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Thermocrinis albus DSM 14484

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_012991515.1 THAL_RS02360 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::P16524
         (393 letters)



>NCBI__GCF_000025605.1:WP_012991515.1
          Length = 371

 Score =  173 bits (438), Expect = 8e-48
 Identities = 114/357 (31%), Positives = 183/357 (51%), Gaps = 13/357 (3%)

Query: 28  EDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNYD 87
           EDV+ + IG+PD   P  V    ++AI E    YT + G  ELRQ +  +       +  
Sbjct: 23  EDVVHMEIGEPDLDPPPGVWEHLERAIKERKYFYTASVGIEELRQKIAEHYWTYYGVDIS 82

Query: 88  AESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTTSHG- 146
            E  ++ITTG+S A    +  ILS GD + +  P YP Y+   +L    P+++       
Sbjct: 83  PE-RVVITTGSSGAFLVVYSIILSAGDSIAIADPSYPCYKNFAHLLDINPILIPVGPETH 141

Query: 147 FKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYSEL 206
           +++T  ++E     N K V +  PSNPTG    E+ L+S+ +    + ++++SDEIY  L
Sbjct: 142 YQITPPMLEGL---NIKAVHISSPSNPTGTFYREDTLRSLCSYCDEKGIYLISDEIYHGL 198

Query: 207 TYDRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCASS 266
            Y+   +++  +  ++ IV+NG SK   M G+R+G++  P D+ +    V Q     A S
Sbjct: 199 VYEGREHTVLEF-SERAIVVNGFSKFFCMPGFRLGWIILPPDLVRKAQIVLQNVFISAPS 257

Query: 267 ISQKAALEAVTNGFDDALI--MREQYKKRLDYVYDRLVSMGLDVVKPSGAFYIFPSIKSF 324
           +SQ AAL A    FD   +  +RE Y++R D +Y  L  +      P G FYI+  +  +
Sbjct: 258 LSQYAALGA----FDYKYLQKVREIYRERRDVLYRELKDVFNIPCPPEGGFYIWADVSRY 313

Query: 325 GMTSFDFSMALLEDAGVALVPGSSFS-TYGEGYVRLSFACSMDTLREGLDRLELFVL 380
              S+ F M LLE A VA+ PG  F       Y+RL++     TL EG  R++ +++
Sbjct: 314 TENSYQFCMDLLEKAKVAVTPGIDFGYNRTNTYIRLAYTKDKGTLLEGARRIKSYLM 370


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: 332
Number of extensions: 10
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: 393
Length of database: 371
Length adjustment: 30
Effective length of query: 363
Effective length of database: 341
Effective search space:   123783
Effective search space used:   123783
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 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