GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS15835
          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:

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