GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Desulfovibrio vulgaris Miyazaki F

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate 8499593 DvMF_0361 LL-diaminopimelate aminotransferase (RefSeq)

Query= BRENDA::Q8YTF2
         (403 letters)



>FitnessBrowser__Miya:8499593
          Length = 389

 Score =  378 bits (970), Expect = e-109
 Identities = 181/380 (47%), Positives = 257/380 (67%), Gaps = 2/380 (0%)

Query: 9   ADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHG 68
           ADR+  LPPY+FA +D++KA+   +G+D+I LG+G+PD  TP  +++A  +A++ P NH 
Sbjct: 7   ADRLATLPPYLFAGIDKVKAEVAARGVDIISLGIGDPDMPTPDFIIEAMKKAVERPANHQ 66

Query: 69  YPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPS 128
           YP + G   FR+ + NWY RR+GV LDP +E + L+GSKEG++H  +A+VNPGD+VLV +
Sbjct: 67  YPSYVGMLEFRQEVANWYGRRFGVSLDPKTEVIGLIGSKEGIAHFPLAFVNPGDLVLVCT 126

Query: 129 PAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAP 188
           P YP +       GG V  + L  END+L DL AIP     +AK+++ NYP+NPT ATAP
Sbjct: 127 PNYPVYHIATGFVGGEVQFIPLVEENDYLPDLDAIPAATWDRAKMIFVNYPNNPTAATAP 186

Query: 189 REFFEEIVAFARKYEILLVHDLCYAELAFD-GYQPTSLLEIPGAKDIGVEFHTLSKTYNM 247
           R F+E+++   RK+ +++ HD  Y E+ +D   +P S+LE+ GAKD+ +EFH+LSKTYNM
Sbjct: 187 RAFYEKLIGICRKHNVIIAHDTAYTEVYYDENDKPMSILEVEGAKDVTIEFHSLSKTYNM 246

Query: 248 AGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRD 307
            GWRVG  VGN  ++ GL  +K N+D GIF A+Q A+  AL+  D +  E++  YR RRD
Sbjct: 247 TGWRVGMAVGNASLVAGLGKVKENVDSGIFQAVQEASIVALRDGDDFCRELRGIYRKRRD 306

Query: 308 FLIQGLGELGWDVPKTKATMYLWVKCPVGMGST-DFALNLLQQTGVVVTPGNAFGVAGEG 366
            ++  L ++G       A  Y+W K P G GS+ +F   +L++TGVV+TPGN FG  GEG
Sbjct: 307 VVVAALNKVGIACRVPTAAFYIWAKVPAGYGSSAEFVTAVLEKTGVVLTPGNGFGTPGEG 366

Query: 367 YVRISLIADCDRLGEALDRI 386
           Y RISL  D DRL EA+ RI
Sbjct: 367 YFRISLTVDTDRLEEAVSRI 386


Lambda     K      H
   0.321    0.140    0.427 

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: 464
Number of extensions: 20
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: 403
Length of database: 389
Length adjustment: 31
Effective length of query: 372
Effective length of database: 358
Effective search space:   133176
Effective search space used:   133176
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