GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE in Herbaspirillum seropedicae SmR1

Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate HSERO_RS15835 HSERO_RS15835 aspartate aminotransferase

Query= CharProtDB::CH_004054
         (397 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS15835 HSERO_RS15835 aspartate
           aminotransferase
          Length = 405

 Score =  417 bits (1072), Expect = e-121
 Identities = 210/398 (52%), Positives = 271/398 (68%), Gaps = 2/398 (0%)

Query: 1   MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60
           +F  ++    DPIL + E +  D    K NL +G+YY+++G +P L+ V +AEA L A+ 
Sbjct: 9   LFSAIEMAPRDPILGVTEAYNADQNPAKTNLGVGVYYDDNGKVPLLECVKKAEAELAAKL 68

Query: 61  HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120
                YLP++GL  Y  A+  L+FGA   V+ ++R  T+Q LGG+GALK+GADFLK + P
Sbjct: 69  -APRTYLPIDGLATYDRAVQELVFGAGSAVVTEKRAITVQALGGTGALKLGADFLKHFSP 127

Query: 121 E-SGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLH 179
             + VW+SDP+WENH A+F  AGF+V+ YP+YD AT GV F  +L  LKT+ + S+VLLH
Sbjct: 128 AGTEVWISDPSWENHRALFEMAGFKVNAYPYYDPATRGVNFAGMLDALKTMKSGSVVLLH 187

Query: 180 PCCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPA 239
            CCHNPTGADLT+DQW  VIE++ +R L+PFLD+AYQGFG G+ ED   +R  A AG P 
Sbjct: 188 ACCHNPTGADLTDDQWTQVIEVVTSRGLVPFLDMAYQGFGDGIAEDGQVVRRFAEAGGPL 247

Query: 240 LVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVL 299
            VSNSFSK FSLYGERVG LS+    AE A RVL QLK  VR NYS+PP  G QVVA  L
Sbjct: 248 FVSNSFSKSFSLYGERVGALSIAAASAEEAARVLSQLKRVVRTNYSNPPIHGGQVVATAL 307

Query: 300 NDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQV 359
               L+  W  E+ EMR RI  MRQ LV  L  + P  +FD+++ QRGMFSY+GL+ AQV
Sbjct: 308 ASPELRKLWEDELAEMRVRIREMRQLLVAKLKEKAPGHDFDFVIKQRGMFSYSGLTKAQV 367

Query: 360 DRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397
           DRLR EF +Y + +GR+CVA LNT N+  V  A A V+
Sbjct: 368 DRLRNEFSIYAVDTGRICVAALNTKNIDVVVDAIAKVL 405


Lambda     K      H
   0.320    0.135    0.401 

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: 410
Number of extensions: 11
Number of successful extensions: 3
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: 397
Length of database: 405
Length adjustment: 31
Effective length of query: 366
Effective length of database: 374
Effective search space:   136884
Effective search space used:   136884
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