GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Caulobacter crescentus NA1000

Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate CCNA_03024 CCNA_03024 branched-chain amino acid aminotransferase

Query= BRENDA::P54691
         (305 letters)



>FitnessBrowser__Caulo:CCNA_03024
          Length = 296

 Score =  128 bits (322), Expect = 1e-34
 Identities = 83/267 (31%), Positives = 140/267 (52%), Gaps = 19/267 (7%)

Query: 9   YFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAK 68
           + + +FVP+ +AK+ V TH LHY ++ F G R            +F+L  H +RL KSA+
Sbjct: 14  WLDGQFVPWREAKVHVLTHGLHYASSVFEGERMYGGE-------IFKLTEHTERLFKSAE 66

Query: 69  FLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVY--SSGLGIAPRLHNLEKDFLVYG 124
            L ++I  +  +I E       KN   K  Y+RP+ +  S  +G++ +   +     V+ 
Sbjct: 67  ILDFEIPYTVAEIDEACKATAAKNGL-KDCYVRPIAWRGSEMIGVSAQQSKIHVAIAVW- 124

Query: 125 LEMGDYL----AADGVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAI 180
            E   Y      A G+    + + R + ++ P+  K +  Y+   ++K  A + G+ +A+
Sbjct: 125 -EWPSYFDPATKAKGIRLTWAKYQRPDPKTAPIAAKAAGLYMICTISKHAAEKDGYADAM 183

Query: 181 LMNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPIDK 240
           +++ +G V EATG NVF V++G + TP      L+GITR +++ +A   GI   +R I K
Sbjct: 184 MLDYRGYVAEATGANVFFVKDGVLHTP-KPDCFLDGITRRTVIDLAKAKGIEVVERHIQK 242

Query: 241 SELMIADEVFLSGTAAKITPVKRIENF 267
            EL    E F+ GTAA++TPV  +  F
Sbjct: 243 EELATFTECFIVGTAAEVTPVSEVGEF 269


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: 221
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: 296
Length adjustment: 27
Effective length of query: 278
Effective length of database: 269
Effective search space:    74782
Effective search space used:    74782
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