GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Desulfovibrio vulgaris Miyazaki F

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate 8501445 DvMF_2175 transcriptional regulator, GntR family with aminotransferase domain (RefSeq)

Query= BRENDA::Q72LL6
         (397 letters)



>FitnessBrowser__Miya:8501445
          Length = 498

 Score =  160 bits (405), Expect = 8e-44
 Identities = 117/379 (30%), Positives = 181/379 (47%), Gaps = 13/379 (3%)

Query: 18  QASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYA 77
           +A  I  +L+      ++ F    P   L P        + ++R +   A  Y+   G  
Sbjct: 113 RARLISTVLEAVGNRDLVPFGVLCPDETLLPGRALGRILSEVMRSRAGEAAAYATIPGDL 172

Query: 78  PLRAFVAEW------IGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQA 131
            LR  +A W      +G  P+++LIT G+ +AL +  +     G  V++++P+Y   +Q 
Sbjct: 173 ELRRQIA-WRHRECGVGAGPDDILITNGAVEALYIALRCLTRPGDIVMIQSPTYYCFLQL 231

Query: 132 FRLQGPRFLTVPAGEE-GPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQ 190
               G R + VP+  E G D   +  +L R R       P+F NP G LTP  A++ +L 
Sbjct: 232 IESLGLRAIEVPSTPEAGVDPRDVRHILDRHRVAACAFSPNFNNPDGSLTPDDAKREILD 291

Query: 191 MVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAV 250
           M+ ERG+ ++EDD   +L++G +R PS F      G   V    SFSK ++PG R+ + V
Sbjct: 292 MLAERGIHLIEDDVSTDLHYGPSR-PSTFLQWDVHGL--VTLCSSFSKTVAPGFRMGWMV 348

Query: 251 AHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSER-LERVRRVYREKAQAMLHALD 309
                 ++  + K   ++    L Q  + E L++G  ER L R+R  +  + QAM   L 
Sbjct: 349 TGRIG-ERAREIKATTNVCGATLTQFAMAEYLRQGLFERQLRRLRTAFSRQMQAMRMHLA 407

Query: 310 REVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRL 369
              P     TRP+GG  +W+ELP G     LF RA +  ++  PG  F       N LRL
Sbjct: 408 DCFPSGTGVTRPEGGGVLWLELPPGTDGVELFFRARQAGISVAPGAVFSTQEKFANYLRL 467

Query: 370 SYATLDREGIAEGVRRLGR 388
               L  E +AEG+R LGR
Sbjct: 468 GCNGLWNERMAEGLRTLGR 486


Lambda     K      H
   0.320    0.139    0.403 

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: 520
Number of extensions: 34
Number of successful extensions: 4
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: 498
Length adjustment: 32
Effective length of query: 365
Effective length of database: 466
Effective search space:   170090
Effective search space used:   170090
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: 51 (24.3 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