GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Salinicoccus carnicancri Crm

Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_017549645.1 C792_RS0111735 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q9RAT0
         (391 letters)



>NCBI__GCF_000330705.1:WP_017549645.1
          Length = 385

 Score =  306 bits (783), Expect = 8e-88
 Identities = 154/389 (39%), Positives = 238/389 (61%), Gaps = 7/389 (1%)

Query: 4   LKKFNPNLDKIEISLIRQFDQQVSSIPDIIKLTLGEPDFYTPEHVKQAGIAAIENNQSHY 63
           + + N  L  + +   RQ   +V+   +II LTLG+PDF  P+ V+   + A++N    Y
Sbjct: 1   MPELNRLLKNVGLPGTRQMANRVAGQTEIIDLTLGQPDFPVPQAVRDRVMQAVDNEPMKY 60

Query: 64  TGMAGLLELRQAASEFLLKKYGLSYAAEDEILVTVGVTEAISSVLLSILVAGDEVLIPAP 123
           +   G++ELR+A ++F   KY   Y   DE++VT G +EA+ ++  +I+  GDEV++PAP
Sbjct: 61  SHNRGMMELRKAITDFYKDKYTAEYEPSDEVIVTNGGSEALDTIFRTIINPGDEVIMPAP 120

Query: 124 AYPGYEPLITLAGGSLVEIDTRANDFVLTPEMLDQAIIEREGKVKAVILNYPANPTGVTY 183
            Y GYEP++T+ GG+ V +DT    F+ T + L+ A+ +R    KAV+LNYP NPTG  Y
Sbjct: 121 VYTGYEPIVTMLGGTAVLVDTTETGFIPTAQKLEAAMTQR---TKAVLLNYPNNPTGAVY 177

Query: 184 NREQIKDLAEVLKKHEVFVIADEVYSELNYTDQPHVSIAEY--APEQTIVLNGLSKSHAM 241
            +  +  L E+ K+H++F++ DE+Y+E N  D  H S   Y    ++ + +NGLSKSHAM
Sbjct: 178 PKGTVASLVELFKRHDIFIVVDEMYAE-NTLDGEHHSFTSYPAIKDRLLAVNGLSKSHAM 236

Query: 242 TGWRIGLIFAARELVAQIIKTHQYLVTSASTQSQFAAIEALKNGADDALPMKKEYLKRRD 301
           TGWRIG +  + E++ ++   H Y    AS  SQ AA+EAL   AD    M   Y +RRD
Sbjct: 237 TGWRIGWLLGSAEMIEKLTLVHLYNTLCASMPSQIAALEALTGAADAPAEMNAAYKERRD 296

Query: 302 YIIEKMSALGFKIIEPDGAFYIFAKIPADLEQDSFKFAVDFAKENAVAIIPGIAFGQYGE 361
           YI  ++  +G + + P+GAFYIF  I     + SF FAV+  +E  VA++PG AF +YGE
Sbjct: 297 YIYRRLVNMGLETVLPEGAFYIFPSIKG-YNESSFDFAVELLEEAGVAVVPGAAFSEYGE 355

Query: 362 GFVRLSYAASMDVIEQAMARLTDYVTKKR 390
           G +R+S+A  M+ +E+A  R+  ++  K+
Sbjct: 356 GHIRISFATGMENLEEAADRMEKFLNGKK 384


Lambda     K      H
   0.318    0.135    0.375 

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: 388
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: 391
Length of database: 385
Length adjustment: 30
Effective length of query: 361
Effective length of database: 355
Effective search space:   128155
Effective search space used:   128155
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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