GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Enterococcus termitis LMG 8895

Align Tyrosine aminotransferase; TAT; L-tyrosine:2-oxoglutarate aminotransferase; EC 2.6.1.5 (characterized)
to candidate WP_069662075.1 BCR25_RS02850 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::Q93703
         (464 letters)



>NCBI__GCF_001730305.1:WP_069662075.1
          Length = 405

 Score =  154 bits (389), Expect = 5e-42
 Identities = 108/371 (29%), Positives = 191/371 (51%), Gaps = 14/371 (3%)

Query: 75  KVIKLHLGDPSVGGKLPPSEIAVQAMHESVSSHMFDGYGPAVGALAAREAIVERYSSADN 134
           +++KL+ G+P+  G   P+E+ V+ M  +V +   +GY  + G  +AR+AI E+Y     
Sbjct: 34  RILKLNTGNPAPFGFDAPNEV-VRDMITNVRNS--EGYSDSKGIFSARKAI-EQYCQVKG 89

Query: 135 V--FTADDVVLASGCSHALQMAIEAVANAGENILVPHPGFPLYSTLCRPHNIVDKPYKID 192
               T +D+   +G S  + M ++ + N G+ +LVP P +PL++            Y  D
Sbjct: 90  FPNVTINDIYTGNGVSELITMCMQGLLNNGDEVLVPMPDYPLWTASVSLAGGNPVHYICD 149

Query: 193 MTGEDVRIDLSYMATIIDDNTKAIIVNNPGNPTGGVFTKEHLEEILAFAHQYKLIIIADE 252
              E    D+  + + +  NTKAI++ NP NPTG ++ KE LE+I+  A Q  LII +DE
Sbjct: 150 EQAE-WNPDIDDIKSKVTSNTKAIVLINPNNPTGALYPKEILEQIVEIARQNDLIIFSDE 208

Query: 253 IYGDLVYNGATFYPLASLSPKVPIITCDGIAKRWMVPGWRLGWLIIHNHFGVLTDVKNGI 312
           IY  LV +G T  P+A+L+P + ++T +G++K   V G+R GW+++  +   +     G+
Sbjct: 209 IYDRLVMDGLTHIPIATLAPDLFVVTLNGLSKSHRVAGFRCGWMVLSGNKKHVKGYIEGL 268

Query: 313 VALSQKIVGPCSLVQGALPKIL--RETPEDYFVYTRNVIETNANIVDSILADVPGMRVVK 370
             L+   +    L Q  +   L   ++ ++  +    V E    I ++I  ++PG+  VK
Sbjct: 269 NMLASMRLCSNVLSQQIIQTALGGYQSVDELLLPGGRVYEQREFIYNAI-NEIPGLSAVK 327

Query: 371 PKGAMYMMVNISRTAYG--SDVSFCQNLIREESVFCLPGQAF--SAPGYFRVVLTCGSED 426
           PK A Y+   I    +    D  F  + + E  +  + G  F  + P +FR+V     ED
Sbjct: 328 PKAAFYIFPKIDTARFDIYDDEKFVLDFLHEHHILLVHGGGFNWTQPDHFRIVYLPKMED 387

Query: 427 MEEAALRIREF 437
           ++  A +++ F
Sbjct: 388 LKLTAEKMQRF 398


Lambda     K      H
   0.319    0.136    0.407 

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: 415
Number of extensions: 23
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: 464
Length of database: 405
Length adjustment: 32
Effective length of query: 432
Effective length of database: 373
Effective search space:   161136
Effective search space used:   161136
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 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