GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Salinicoccus carnicancri Crm

Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_017549034.1 C792_RS0108435 glutamate-1-semialdehyde 2,1-aminomutase

Query= SwissProt::H8WR05
         (434 letters)



>NCBI__GCF_000330705.1:WP_017549034.1
          Length = 428

 Score =  207 bits (527), Expect = 5e-58
 Identities = 137/418 (32%), Positives = 203/418 (48%), Gaps = 22/418 (5%)

Query: 24  SQRQFEAQARYMPGANSRSVLFYAPF---PLTIARGEGAALWDADGHRYADFIAEYTAGV 80
           S+  ++     MPG  +  V  +      P+ I   + A  +D DG+ Y D++  +   +
Sbjct: 5   SKALYKKATELMPGGVNSPVRAFNSVGMDPVFIDHAKDARTYDVDGNEYIDYVLSFGPLI 64

Query: 81  YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140
            GHS   + DAV EA Q G +      LE  LA L+ +R P +E +R  +SGTEA L AL
Sbjct: 65  LGHSDDRVVDAVSEAAQKGTSFGAPTSLENELAELVIDRVPSVEMIRMVSSGTEATLAAL 124

Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTT---VPFDFLVLPYND 186
             A  FTGR KI+ F G YHG           GV   G   SP        + + +PYND
Sbjct: 125 RLARGFTGRSKILKFEGCYHGHSDSLLIKAGSGVATLGLPDSPGVPEGTAANTITVPYND 184

Query: 187 AQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS- 245
            ++ +   ++ G +IA V++EP+ G  G +P    +L  +R    + G LL+FDEVMT  
Sbjct: 185 EESLKEAFDQFGEDIAAVIMEPVAGNMGVVPPVEGYLDFVRRITEENGTLLIFDEVMTGF 244

Query: 246 RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNNV 305
           R+  +      GI  DLT LGK IGGG+  GA+GGR D+M    P TG +  +GT + N 
Sbjct: 245 RVGYNCAQGHYGITPDLTCLGKVIGGGLPVGAYGGRRDIMEHIAP-TGDIYQAGTLSGNP 303

Query: 306 MTMAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQG 365
           + M AG   L +L TPE+       G+ L   L  + + +G  +     GS++     +G
Sbjct: 304 LAMTAGLETLKQL-TPESYEYFNRLGDMLENGLKEIFSEKGYPITVNRAGSMIGFFLTEG 362

Query: 366 DVRSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGF--VVLSLPLTDADIDRYVAAIGS 421
            V   +     D  L   ++  LL E +Y  P  F  + LS   T+ DI + + A  +
Sbjct: 363 PVTDFDSANTSDLDLFAQMYRSLLEEGVYLPPSQFEGMFLSTKHTEEDISKTLTAFSN 420


Lambda     K      H
   0.322    0.138    0.408 

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: 17
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: 434
Length of database: 428
Length adjustment: 32
Effective length of query: 402
Effective length of database: 396
Effective search space:   159192
Effective search space used:   159192
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: 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