GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapX in Desulfovibrio vulgaris Miyazaki F

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate 8501474 DvMF_2204 aminotransferase class I and II (RefSeq)

Query= SwissProt::P16524
         (393 letters)



>lcl|FitnessBrowser__Miya:8501474 DvMF_2204 aminotransferase class I
           and II (RefSeq)
          Length = 390

 Score =  229 bits (584), Expect = 1e-64
 Identities = 139/381 (36%), Positives = 215/381 (56%), Gaps = 24/381 (6%)

Query: 5   LNPKAREIEISGIRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPN 64
           +N KA E++  G++           V+SL +G+PDF TP HV+ AAK AID+  T YT  
Sbjct: 18  VNAKALELKAKGVQ-----------VVSLAVGEPDFPTPEHVREAAKTAIDQGFTRYTQV 66

Query: 65  AGYLELRQAVQLYMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYP 124
            G  ELRQAV  Y  +        E+ ++ T G  QA+   F+ +L+PGDEV++P P + 
Sbjct: 67  PGIPELRQAVCGYFARFYGVEAPMEATVV-TNGGKQALYNLFQCLLNPGDEVLVPAPYWV 125

Query: 125 GYEPIINLCGAKPVIVDTTSH-GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEEL 183
            Y  ++ L G  PV V + +  GFK+T   ++ A+TP T+ ++L  PSNPTG   S  E 
Sbjct: 126 SYPALVELAGGVPVFVASPAERGFKVTPEELDRAVTPKTRVLLLNSPSNPTGACYSRAET 185

Query: 184 KSIAALLKGRNVFVLSDEIYSELTYDRPH-YSIATYLR---DQTIVINGLSKSHSMTGWR 239
            +I      R++FV+SDEIY  L Y+     S+  +     +   V+NGL+K+ +MTGWR
Sbjct: 186 DAIMEWAIARDLFVVSDEIYDRLVYEPAEAVSVCDWWERHPENVAVVNGLAKTFAMTGWR 245

Query: 240 IGFLFAPKDIAKHILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYD 299
           +G+  A  D+ K + K+   + S   S++QKAAL A+T  +D    M++ +++R D  + 
Sbjct: 246 VGYALAHPDLIKAMTKIQGQSTSNICSVAQKAALAALTGPYDAVEEMKKSFRRRRDLAHG 305

Query: 300 RLVSM-GLDVVKPSGAFYIFPSIKSFGMTSFDFSMAL----LEDAGVALVPGSSFSTYGE 354
            + S  G+   KP GAFY+F  +++    +   S +L    +E A VALVPG++F    +
Sbjct: 306 IVSSWPGVICPKPDGAFYLFADMRALFTPALPDSASLCTYIMEQANVALVPGAAFG--DD 363

Query: 355 GYVRLSFACSMDTLREGLDRL 375
             +R S+A S DTL   LD++
Sbjct: 364 ACLRFSYAVSDDTLMIALDKV 384


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: 362
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: 390
Length adjustment: 31
Effective length of query: 362
Effective length of database: 359
Effective search space:   129958
Effective search space used:   129958
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 paper from 2022 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