GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Sinorhizobium meliloti 1021

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate SMc04386 SMc04386 aspartate aminotransferase B protein

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__Smeli:SMc04386
          Length = 410

 Score =  224 bits (571), Expect = 3e-63
 Identities = 143/365 (39%), Positives = 211/365 (57%), Gaps = 24/365 (6%)

Query: 30  VISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNYDAE 89
           VI L  G+PDF TP HVK AA  AI    T YT   G  EL++A++   +++    Y+ +
Sbjct: 43  VIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAIREKFQRENGLAYELD 102

Query: 90  SEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT-TSHGFK 148
            EI + TGA Q +  A    L PGDEVI+P P +  Y  I+++C  KPV++    S GF+
Sbjct: 103 -EITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEGKPVLIACDASSGFR 161

Query: 149 LTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLKGRNVFVLSDEIYSELT 207
           LTA  +E A+TP T+ V+L  PSNP+G   S  + + +   LL+  +V++L D++Y  + 
Sbjct: 162 LTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHPHVWLLVDDMYEHIV 221

Query: 208 YDRPHY----SIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSC 263
           YD   +     +   L+++T+ +NG+SK+++MTGWRIG+   P+++ K +  V     SC
Sbjct: 222 YDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPRELIKAMAVVQSQATSC 281

Query: 264 ASSISQKAALEAVTNGFDDALIMR-EQYKKRLDYVYDRLVSM-GLDVVKPSGAFYIF--- 318
            SSISQ A++ A+ NG  D L  R E +++R D V + L ++ GLD   P GAFY F   
Sbjct: 282 PSSISQAASVAAL-NGPQDFLKERTESFQRRRDLVVNGLNAIDGLDCRVPEGAFYTFSGC 340

Query: 319 --------PSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLRE 370
                   PS K    T  DF   LLEDA VA+VPGS+F      + R+S+A S   L+E
Sbjct: 341 AGVLGKVTPSGKRI-KTDTDFCAYLLEDAHVAVVPGSAFGL--SPFFRISYATSEAELKE 397

Query: 371 GLDRL 375
            L+R+
Sbjct: 398 ALERI 402


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: 382
Number of extensions: 18
Number of successful extensions: 7
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: 410
Length adjustment: 31
Effective length of query: 362
Effective length of database: 379
Effective search space:   137198
Effective search space used:   137198
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:

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