GapMind for Amino acid biosynthesis

 

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

Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_066326841.1 BLR17_RS05750 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::A3PMF8
         (400 letters)



>NCBI__GCF_900100165.1:WP_066326841.1
          Length = 396

 Score =  379 bits (973), Expect = e-110
 Identities = 203/395 (51%), Positives = 261/395 (66%), Gaps = 3/395 (0%)

Query: 4   LSDTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTK 63
           LSD +  +  SQT+A+   AREL A G+D+I L  GEPDF+TPD IK AAK+AID   + 
Sbjct: 5   LSDRINNLATSQTLAMAALARELKAQGKDIISLSLGEPDFNTPDFIKEAAKKAIDENYST 64

Query: 64  YTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPAP 123
           Y+ VDG  ELK AIC KF+R+NGL Y P+Q+ V TG KQ LYN     LN GDEVI+PAP
Sbjct: 65  YSPVDGYAELKDAICRKFKRDNGLDYKPSQIVVSTGAKQSLYNIAQVMLNDGDEVILPAP 124

Query: 124 YWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTR 183
           YWVSY ++V L+GG PV V   +ET FK+TPEQLEAAITP+TK   F+SP NP+G+ Y R
Sbjct: 125 YWVSYFEIVKLSGGVPVEVPTSVETDFKITPEQLEAAITPKTKMMWFSSPCNPSGSVYNR 184

Query: 184 AELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCM 243
            EL AL +VL ++P +++++D++YEH+ F    F + A I PG+++RT+T NGV+KA+ M
Sbjct: 185 EELTALAKVLEKYPNIYVVADEIYEHINFSG-TFCSIASI-PGMFERTVTVNGVAKAFAM 242

Query: 244 TGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRD 303
           TG+RIGY   P  + +A   IQ Q TS   SIAQ A + A+      L    +AF  RRD
Sbjct: 243 TGYRIGYIGAPEFIAKACTKIQGQVTSGANSIAQRATITAVDADPSVLNHMVQAFHSRRD 302

Query: 304 LVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVV 363
           LVV +L E  G+    PEGAFYV+PD+S   GKT   G +I D    +  LL E  VA V
Sbjct: 303 LVVGLLKEIPGIKINVPEGAFYVFPDVSSFFGKT-LKGTEIKDANDVSMYLLAEANVATV 361

Query: 364 FGAAFGLSPNFRISYATADEVLREACARIQAFCAG 398
            G AFG     R SYAT+DE+L+EA  RI+   AG
Sbjct: 362 TGDAFGNPNCIRFSYATSDELLKEALKRIKDALAG 396


Lambda     K      H
   0.318    0.134    0.399 

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: 456
Number of extensions: 15
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: 400
Length of database: 396
Length adjustment: 31
Effective length of query: 369
Effective length of database: 365
Effective search space:   134685
Effective search space used:   134685
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 (21.7 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