GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Azospirillum brasilense Sp245

Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate AZOBR_RS16425 AZOBR_RS16425 branched-chain amino acid aminotransferase

Query= BRENDA::P54691
         (305 letters)



>FitnessBrowser__azobra:AZOBR_RS16425
          Length = 290

 Score =  124 bits (312), Expect = 2e-33
 Identities = 86/274 (31%), Positives = 141/274 (51%), Gaps = 21/274 (7%)

Query: 7   IAYFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKS 66
           + +++   VP+ DA + V +H LHY +  F G R        GT+  F+L  H +RL+ S
Sbjct: 12  VIWYDGALVPWRDANLHVLSHGLHYASCVFEGERVYN-----GTV--FKLTEHSERLAAS 64

Query: 67  AKFLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVY--SSGLGIAPRLHNLEKDFLV 122
           A+ L +++  S  +I     + VK        Y+RP+ +  S  +G+A +   +     V
Sbjct: 65  ARILGFELPYSVAEIDAATNETVKA-MGFTDAYVRPVAWRGSEMMGVAAQASRIHVAIAV 123

Query: 123 YGLEMGDYLAAD----GVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDE 178
           +  +   Y + +    G+    S W R      P   K +  Y+   L+K EA   G+ +
Sbjct: 124 W--QWPSYFSPEAKMAGIKLTWSRWRRPAPDMAPTASKAAGLYMICTLSKHEAEAEGYQD 181

Query: 179 AILMNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPI 238
           A++++ +G + EATG N+F+V +G+I TP      L+GITR +++ +A   GI   +R I
Sbjct: 182 ALMLDYRGYLAEATGANLFLVMDGKIHTP-KPDCFLDGITRRTVIDLAKARGIEVIERHI 240

Query: 239 DKSELMIADEVFLSGTAAKITPVKRI--ENFTLG 270
              EL    EVFL+GTAA++TPV +I    FT G
Sbjct: 241 QPDELANTQEVFLTGTAAEVTPVGQIGDHRFTPG 274


Lambda     K      H
   0.320    0.138    0.406 

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: 206
Number of extensions: 11
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: 305
Length of database: 290
Length adjustment: 26
Effective length of query: 279
Effective length of database: 264
Effective search space:    73656
Effective search space used:    73656
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: 48 (23.1 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