GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Enterococcus termitis LMG 8895

Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_069661945.1 BCR25_RS02115 pyridoxal phosphate-dependent aminotransferase

Query= CharProtDB::CH_004890
         (393 letters)



>NCBI__GCF_001730305.1:WP_069661945.1
          Length = 396

 Score =  427 bits (1098), Expect = e-124
 Identities = 213/394 (54%), Positives = 278/394 (70%), Gaps = 1/394 (0%)

Query: 1   MKLAKRVSALTPSTTLAITAKAKELKAAGHDVIGLGAGEPDFNTPQHIIDAAVRSMNEGH 60
           M ++ R   L PS TLA +AKA  LKA G +V+ L  GEPDF TP++I  AA++++  G 
Sbjct: 1   MDISMRAQKLEPSVTLAASAKANALKAQGQNVLSLTVGEPDFTTPKNIQQAAIQAIESGK 60

Query: 61  TKY-TPSGGLAELKNSIAEKFKRDQNIEYKPSQIIVCTGAKHALYTLFQVILDEEDEVII 119
             Y TPS G+ EL+ ++A   K +  ++Y+   +IV  GAK ALY LFQ +L+  DEVII
Sbjct: 61  ASYYTPSAGIKELRQAVATYIKSNYQLDYQVENVIVTDGAKFALYLLFQAVLNPLDEVII 120

Query: 120 PTPYWVSYPEQVKLAGGKPVYVEGLEENHFKISPEQLKNAITEKTKAIVINSPSNPTGVM 179
           P PYWVSY EQVKLA G PV+V   +E  FK++  QL+ A TEKTK +++NSPSNPTG++
Sbjct: 121 PVPYWVSYGEQVKLAEGVPVFVSCAQEQEFKVTVAQLEEARTEKTKILILNSPSNPTGMI 180

Query: 180 YTEEELSALGEVCLEHDILIVSDEIYEKLTYGGKKHVSIAQLSDRLKEQTVIINGVSKSH 239
           Y+E+EL A+GE  + HDILIVSD+IY KL Y G     IA LS+ +++QT+IINGVSKS+
Sbjct: 181 YSEKELRAIGEWAVLHDILIVSDDIYGKLVYNGAVFTPIATLSEAIQKQTIIINGVSKSY 240

Query: 240 SMTGWRIGYAAGSEDIIKAMTNLASHSTSNPTSIAQYGAIAAYNGPSEPLEEMREAFEHR 299
           +MTGWRIGYA G + II  M ++AS STSNPT+++QY AI A +G  + +E MR+AFE R
Sbjct: 241 AMTGWRIGYAVGDKAIIATMNDIASQSTSNPTAVSQYAAIEALSGEQDTVETMRQAFEER 300

Query: 300 LNTIYAKLIEIPGFSCVKPEGAFYLFPNAKEAAQSCGFKDVDEFVKALLEEEKVAIVPGS 359
           LN +Y     +PGF   KP GAFYLFPN KE    CG+ DV ++V  LL E  VA+V G+
Sbjct: 301 LNKVYPMFAALPGFKIEKPHGAFYLFPNIKETMDLCGYTDVTDWVDDLLAEAHVALVTGA 360

Query: 360 GFGSPENVRLSYATSLDLLEEAIERIKRFVEKHS 393
           GFG+PENVR+SYAT LD LEEA+ RI  F+E  S
Sbjct: 361 GFGAPENVRISYATDLDTLEEAVARIAAFIEAKS 394


Lambda     K      H
   0.313    0.131    0.370 

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: 18
Number of successful extensions: 2
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: 393
Length of database: 396
Length adjustment: 31
Effective length of query: 362
Effective length of database: 365
Effective search space:   132130
Effective search space used:   132130
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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