GapMind for Amino acid biosynthesis

 

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

Align Transaminase BacF; Transaminase A; EC 2.6.1.- (characterized)
to candidate WP_066328699.1 BLR17_RS00150 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::P39643
         (399 letters)



>NCBI__GCF_900100165.1:WP_066328699.1
          Length = 381

 Score =  276 bits (706), Expect = 7e-79
 Identities = 146/381 (38%), Positives = 221/381 (58%), Gaps = 2/381 (0%)

Query: 3   ITPSDVIKTLPRQEFSLVFQKVKEMEKTGAHIINLGQGNPDLPTPPHIVEALREASLNPS 62
           IT ++ + T+    FS   ++V+++   G  IIN+G G+PDL     +++A+  A  + +
Sbjct: 2   ITTANRLNTVEEYYFSSKLREVRQLAAEGKPIINMGIGSPDLAPAQAVIDAVALAMQDVN 61

Query: 63  FHGYGPFRGYPFLKEAIAAFYKREYGVTINPETEVALFGGGKAGLYVLTQCLLNPGDIAL 122
            HGY  ++G P L++++A FY+  + V +NP TE+    G K G+  ++   LN GD  L
Sbjct: 62  AHGYQSYQGLPELRKSMADFYQNNFQVALNPNTEILPLMGSKEGIMHISMAFLNEGDQVL 121

Query: 123 VPNPGYPEYLSGITMARAELYEMPLYEENGYLPDFEKIDPAVLEKAKLMFLNYPNNPTGA 182
           +PNPGYP Y S   +  AE     L E N + PDFE ++   L K KLM++ YP+ PTGA
Sbjct: 122 IPNPGYPTYTSVTNLVGAEAVYYDLAEANNWEPDFEALEKLDLSKVKLMWIGYPHMPTGA 181

Query: 183 VADAAFYAKAAAFAKEHNIHLIHDFAYGAFEFDQKPASFLEAEDAKTVGAELYSFSKTFN 242
               A + K  AFAK+H I L++D  Y +F  +  P S L+ E AK V  EL S SKTFN
Sbjct: 182 RGSLALFEKLVAFAKKHQILLVNDNPY-SFVLNDNPMSLLQVEGAKEVALELNSLSKTFN 240

Query: 243 MAGWRMAFAVGNEKIIQAVNEFQDHVFVGMFGGLQQAASAALSGDPEHTESLKRIYKERI 302
           MAGWR+    GN ++I AV   + ++  GMF G+Q+ A  AL  D     S+  IYK+R 
Sbjct: 241 MAGWRVGMVSGNAELIDAVLRVKSNMDSGMFFGIQKGAIEALKSDKSWFNSMNEIYKKRR 300

Query: 303 DFFTALCEKELGWKMEKPKGTFYVWAEIPNTFETSHQFSDYLLEHAHVVVTPGEIFGSNG 362
                L EK LG K+ K     +VWA++P   E++ +F D +L   ++ + PG IFGSNG
Sbjct: 301 VLTEQLAEK-LGCKVYKEGVGLFVWAKLPEGIESAEKFIDQILHEKYIFIAPGTIFGSNG 359

Query: 363 KRHVRISMVSKQEDLREFVTR 383
           + ++R ++  K+E ++E + R
Sbjct: 360 EGYIRFALCVKEEKVQEAIDR 380


Lambda     K      H
   0.319    0.137    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: 389
Number of extensions: 17
Number of successful extensions: 3
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: 399
Length of database: 381
Length adjustment: 30
Effective length of query: 369
Effective length of database: 351
Effective search space:   129519
Effective search space used:   129519
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