GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Flavobacterium glycines Gm-149

Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_066329202.1 BLR17_RS10870 pyridoxal phosphate-dependent aminotransferase

Query= curated2:Q60317
         (375 letters)



>NCBI__GCF_900100165.1:WP_066329202.1
          Length = 398

 Score =  171 bits (433), Expect = 3e-47
 Identities = 125/397 (31%), Positives = 206/397 (51%), Gaps = 36/397 (9%)

Query: 2   ISSRCKNIKPSAIR------EIFNLATSDCINLGIGEPDFDTPKHIIEAAKRALDEGKTH 55
           IS R + +  S IR      +I N       +L IG+PD  +P+  I+A K  ++     
Sbjct: 4   ISIRGRRMPESPIRKLAPFADIANKKGLKVYHLNIGQPDIKSPEIAIQAIKN-INMDIIE 62

Query: 56  YSPNNGIPELREEISNKLKDDYNLDVDKDNIIVTCGASEALMLSIMTLIDRGDEVLIPNP 115
           Y P+ G    R +++ +   + N+ VD  +I++T G SEAL+ ++ +++D GDEV+IP P
Sbjct: 63  YGPSAGYESYRRKLA-QFYTNQNVRVDFADIMITTGGSEALLFALGSIMDPGDEVIIPEP 121

Query: 116 SFVSYFSLTEFAEGKI--KNIDLDENFNI-DLEKVKESITKKTKLIIFNSPSNPTGKVYD 172
            + +Y + +E +   +   N D +E F +  +E  ++ IT KTK II  +PSNPTG +Y 
Sbjct: 122 FYANYHAFSEESSATVIPVNSDFEEGFTLPSIEAFEKLITPKTKAIIICNPSNPTGNLYS 181

Query: 173 KETIKGLAEIAEDYNLIIVSDEVYDKIIYDKK--HYSPMQ---FTDRCILINGFSKTYAM 227
           +  I+ L E+ + ++L +++DEVY + IYD+K  HYS M         I+I+  SK Y+M
Sbjct: 182 ESEIQQLGELVKKHDLFLIADEVYREFIYDEKDRHYSVMNLIGLEQNVIMIDSVSKRYSM 241

Query: 228 TGWRIGYLAVSDELNKELDLINNMIKIHQYSFACATTFAQYGALAALRGSQKCVEDMVRE 287
            G RIG +     + K  ++I   +K  Q +  C  T  Q    AA+   +   +++++E
Sbjct: 242 CGARIGCM-----VTKNKEVIATAMKFAQ-ARLCPPTIEQIACEAAIDTPKSYFDEVIKE 295

Query: 288 FKMRRDLIYNGLKDI--FKVNKPDGAFYIFPDVSEYGDGVEV-AKKLIEN------KVLC 338
           +K RRD +   L  I   KV  P  AFY   ++    D  E  A+ L+E+       V+ 
Sbjct: 296 YKDRRDTLITELLKIEGVKVTPPKAAFYCIAELPV--DNTETFAQWLLESYNLNGETVMV 353

Query: 339 VPGVAFGEN---GANYIRFSYATKYEDIEKALGIIKE 372
            P   F      G   +R +Y    ED+ KA+ I+K+
Sbjct: 354 APAAGFYSTPGMGLKQVRIAYVLNKEDLTKAVHILKD 390


Lambda     K      H
   0.318    0.138    0.397 

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: 350
Number of extensions: 22
Number of successful extensions: 6
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: 375
Length of database: 398
Length adjustment: 30
Effective length of query: 345
Effective length of database: 368
Effective search space:   126960
Effective search space used:   126960
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