Aligments for a candidate for tyrB in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Aligments 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for Amino acid biosynthesis