GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Pseudomonas fluorescens GW456-L13

Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate PfGW456L13_4910 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= SwissProt::Q940M2
         (476 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4910
          Length = 413

 Score =  197 bits (501), Expect = 6e-55
 Identities = 128/403 (31%), Positives = 211/403 (52%), Gaps = 41/403 (10%)

Query: 74  YYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTI 133
           Y    L+  +G    L+D++GR YLDA AG+   + GH HP I+ AITEQ+ LL H + +
Sbjct: 32  YQPLALSFNKGLGTRLWDQAGREYLDAVAGVAVTNVGHSHPKIVAAITEQAGLLLHTSNL 91

Query: 134 YLHHAIGDFAEALAAKMP--GNLKVVYFVNSGSEANELAMMMARLYTG--SLE---MISL 186
           Y      D+ + LA K+     +   +F NSG+EANE A+ +ARL+     +E   ++ +
Sbjct: 92  YSI----DWQQRLAQKLTQLAGMDRAFFNNSGAEANETALKIARLHGWHKGIEQPLVVVM 147

Query: 187 RNAYHGGSSNTIGLT---ALNTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDHI 243
            NA+HG +  T+  +   A+      LP          D  +  FG  G+L      D +
Sbjct: 148 ENAFHGRTLGTLSASDGPAVRLGFNKLPG---------DFVKVPFGDLGAL------DKV 192

Query: 244 EYGTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHY 303
           +     ++   + E IQG  G     PGYL +V E+      + + DE+QTG GRTG  +
Sbjct: 193 QQAFGSRIVAVLMEPIQGESGVQLAPPGYLSAVRELCNRRSWLLMLDEIQTGIGRTGQ-W 251

Query: 304 WGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAGGLAV 363
           + FQ + +VPD++T+AKG+GNG+P+GA +   + A +       +TFGGNP+    G  V
Sbjct: 252 FAFQHEGIVPDVMTLAKGLGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTV 311

Query: 364 LNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKA 423
           L++++++   E+    G+ L++RL+     +  +  +RG+GLM+GIEL    +D +   A
Sbjct: 312 LDIVEEQGLLENARLQGARLLERLRTELAGNPNVSQIRGQGLMIGIELKQPIRDLSLIAA 371

Query: 424 ETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLV 466
                    R+ G+L+      GN  R+ PP+   + + + +V
Sbjct: 372 ---------RDHGLLINV--TRGNTIRLLPPLTLDEREVEMIV 403


Lambda     K      H
   0.320    0.138    0.412 

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: 437
Number of extensions: 19
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: 476
Length of database: 413
Length adjustment: 32
Effective length of query: 444
Effective length of database: 381
Effective search space:   169164
Effective search space used:   169164
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