GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Phaeobacter inhibens BS107

Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate GFF3088 PGA1_c31390 putative aromatic-L-amino-acid decarboxylase

Query= BRENDA::H7CE71
         (509 letters)



>FitnessBrowser__Phaeo:GFF3088
          Length = 470

 Score =  307 bits (786), Expect = 6e-88
 Identities = 165/483 (34%), Positives = 261/483 (54%), Gaps = 22/483 (4%)

Query: 26  EFRKQGHMVIDFIADYYQNIEKYPVLSRVEPGYLKKCLPESAPYDPEPISTILKDVQDHI 85
           +F   G  + D+  DY+Q +   PV +R EPG +   LP + P   E +  I  D +  +
Sbjct: 5   DFSYWGRKIADWTQDYHQTVGDRPVRARTEPGDVLNALPATPPETGEDMEAIFADFETVV 64

Query: 86  VPGLTHWQSPNFFAYFSSTASTAGFLGEILTTGFNVVGFNWVSSPAATELENIVMDWLGD 145
           +PG+THWQ P FFAYF+S A+    L E LT+        W +SPAATE+E  +MDWL  
Sbjct: 65  MPGITHWQHPRFFAYFTSNAAAPSVLAEFLTSAIAPQCMLWQTSPAATEMETRMMDWLRQ 124

Query: 146 MLQLPKSFHFSGNGGGVLHGSTCEAIVCTMVAARDQMLRRIGSEN----LGKLVVYGSDQ 201
            L LP+ F       GV+  S   A +  ++  R++ L   G+E        L +Y S +
Sbjct: 125 ALDLPEEFQ------GVIQDSASSATLAAVLTMREKALNWQGNEQGLFAQKTLRIYCSSE 178

Query: 202 THSTLQKATQIVGINTENFRAIKTTKSTGFALSPEMLRLTISSDLEKGLVPLFLCATIGT 261
            H+++ +A  + GI  +N   +   K     + PE L   I +D+  G  P  +   +G 
Sbjct: 179 VHTSVDRAIWVAGIGQQNLVRVPI-KGDWRGMDPEALDAAIEADIAVGHQPAGVILCVGG 237

Query: 262 TATTAIDPLEALCHVAKEYGVWVHVDAAYAGSACICPEFRHFINGVEGANSFSFNPHKWL 321
           T   A DP++ +  VA++YG++ HVDAA+AGSA ICPE+R +  G+E A+S  FNPHKWL
Sbjct: 238 TGVGATDPVDQVLDVAEKYGLYTHVDAAWAGSAMICPEYRDYWPGIERADSIVFNPHKWL 297

Query: 322 FTGMDCCCLWVKNPSVLASSLSTNPEFLRNKASDSKQVVDYKDWQIALSRRFRALKLWLV 381
               DC   ++K+P  L  +L+ +PE+L+    D   +++Y +W + L RRFRALK+W +
Sbjct: 298 GVQFDCSAHFLKDPDDLVRTLAISPEYLKTHGKDG--IINYSEWSVPLGRRFRALKIWFL 355

Query: 382 LRSYGVANLRNFIRIHVNMAKTFEGLVRMDKRFEILVPRNFSLVCFRISPSALISSNEDD 441
           +R+YG+  LR  +R HV  ++     ++ +  FEI+ P  +SL  FR  P+         
Sbjct: 356 IRTYGLEGLRQRLRNHVTWSQQLHDRLKSEPDFEIVTPPMWSLWSFRYQPNGAAD----- 410

Query: 442 EIGMVNEVNCKLLEAINASGKAYMTHAVVGGLYVLRCAVGATLSEEKHIVEAWKVVQDHA 501
               ++++N +L+ AIN  G+ Y+T   V G  V+R   G   + E  ++ A  V+ + A
Sbjct: 411 ----LDDLNLRLVNAINDDGRIYLTQTRVDGALVIRFQAGQFETTEADVMMAHDVITEIA 466

Query: 502 KAI 504
           + +
Sbjct: 467 RTL 469


Lambda     K      H
   0.321    0.135    0.416 

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: 588
Number of extensions: 21
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: 509
Length of database: 470
Length adjustment: 34
Effective length of query: 475
Effective length of database: 436
Effective search space:   207100
Effective search space used:   207100
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 (21.9 bits)
S2: 52 (24.6 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