GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Chlorobaculum parvum NCIB 8327

Align Phosphoserine aminotransferase; EC 2.6.1.52 (characterized, see rationale)
to candidate WP_012503202.1 CPAR_RS10040 alanine--glyoxylate aminotransferase family protein

Query= uniprot:F9VNX9
         (372 letters)



>NCBI__GCF_000020505.1:WP_012503202.1
          Length = 379

 Score =  144 bits (363), Expect = 4e-39
 Identities = 103/338 (30%), Positives = 165/338 (48%), Gaps = 8/338 (2%)

Query: 2   LLIPGPVEVPRSVR-EASTLVVNHRSEKFREIVRKLESLMNKHFSASR-TALLTGSGTLA 59
           L  PGP  VP +V    +  +++HR+ +F EI+ ++   +   F  ++   ++T SGT  
Sbjct: 5   LFTPGPTPVPENVMLRMAAPIIHHRNPEFMEILERVHQDLQYLFRTTQPVVVMTCSGTGG 64

Query: 60  VEAMVYSLIKPNEKVISFPYGEFGNRLVDSLRRRGAQVKVYEKKIGEIFSIDEIKKALDE 119
           +EA + SL    +KVI+   G+FG R  +  R         +   G   + + + + L E
Sbjct: 65  MEAAISSLFTRGDKVITVNGGKFGERWGELARIFTGNCVEEKVAWGSAITTERMVELLKE 124

Query: 120 NKDATAVALVHNETSSGMAFRNLEDVVSEVKRRGLKLLVDSVSGFAAYKLLVNEWKIDAV 179
           +  A  V + H+ETS+G A        +  +     +LVD ++   A++   ++W  D  
Sbjct: 125 HPGAMGVCITHSETSTGTASDVKALCAAIHEHSDALILVDGITAIGAHEFRFDDWGADIC 184

Query: 180 ATGSQKALASVPGMSFVALSDDGIEEIQG-ESLPSY-LDISLHLKFQDKGETPFTPAVGV 237
            TGSQK L   PG++ VA+S+   + I   + LP Y L +   LK     +TPFTPAV +
Sbjct: 185 ITGSQKGLMMPPGLALVAISERAQDVINNRKGLPQYYLSLKKALKSHAGNDTPFTPAVSL 244

Query: 238 FNASLRAAELLEIEGIENRWKRHEACARFVREVLSSYGFLLFGNENNFSNTVVAGVPPIP 297
                 A +++  EGIEN WKRHE  A   R    + G  LF    +++ T V  +P   
Sbjct: 245 IIGLDEALQMVRAEGIENVWKRHEQLAEACRLGCQALGMELFSESPSYAVTAV-WLPEGA 303

Query: 298 DYRK---KLLNEFNIEISGGMGELKEKIVRIGLLGVVD 332
           D+++    L  E  I ++ G  + K KI RI  LG  D
Sbjct: 304 DWKQFNNTLKIENGITVAAGQDDFKGKIFRISHLGYYD 341


Lambda     K      H
   0.316    0.135    0.377 

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: 289
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: 372
Length of database: 379
Length adjustment: 30
Effective length of query: 342
Effective length of database: 349
Effective search space:   119358
Effective search space used:   119358
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 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