GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Methanosarcina mazei Go1

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_011032197.1 MM_RS01335 pyridoxal phosphate-dependent aminotransferase

Query= curated2:B8CX89
         (389 letters)



>NCBI__GCF_000007065.1:WP_011032197.1
          Length = 380

 Score =  218 bits (556), Expect = 2e-61
 Identities = 125/377 (33%), Positives = 206/377 (54%), Gaps = 5/377 (1%)

Query: 6   RIKNLPPYLFAEIDKMIARAKKEGVDVISFGIGDPDQPTPDNIINKMIEAVKDPSTHSYP 65
           R+K +       I  +  R  KEG DVI+F +G+PD  TP NI +   +A+ +  TH  P
Sbjct: 5   RLKRVEESATIRISNIATRMIKEGTDVINFSLGEPDFDTPKNICDAAAKAMYEGKTHYAP 64

Query: 66  SYEGMYEYRKTVADWYKNNYGRELDPDKEVVSLIGSKEGIAHLPFCYINPGDIALVPDPG 125
           S  G+ E R  +A+  +     ++  +K+V+   G+K+GI  +    ++ GD AL+ DP 
Sbjct: 65  S-AGIPELRSAIAEKLRTENHLDVS-EKDVLVTPGAKQGIFEIMMGSLDDGDQALLFDPA 122

Query: 126 YPVYKTSVLLAGGKPVQVPLVEENNFLPDLKAIDEDIARKAKLFFINYPNNPTGAIAPEE 185
           +  Y   +  AG   V VP V E  FLPD  A  E I  K KL  +N P NPTG +  ++
Sbjct: 123 WVTYDACIRFAGADTVWVPTVPEKGFLPDNFA--EYINDKTKLIVVNSPGNPTGGVFGKK 180

Query: 186 FYEELIDFADKYDIIIAHDAAYSEIGLDGYNPPSFMQFEGAKKVGIEFNSLSKPFNMTGW 245
             + + D A  +D+++  D  Y +I  D  +  S   F+G ++  I  N  SK + MTGW
Sbjct: 181 TLQCIADIAIDHDLLVVSDEIYEKIIYDREHI-SIGSFDGMQERTITVNGFSKAYAMTGW 239

Query: 246 RVGWAVGRSDVIESLGRIKTNIDSGIFEAIQYAGIEALTGPEDNIEKMTELYSKRRDLLV 305
           R+G+     ++ + L +I+++  S     +QY G+EAL GP++ ++ M + +  RRD+L+
Sbjct: 240 RLGYLTAPPEIFKLLQKIQSHSVSSATTFVQYGGLEALQGPQEGVKAMVDRFKMRRDILI 299

Query: 306 EGLRELGWEVPVNKATFYIWAKVPEGYNSTEFSTHVFEKTGIFFTPGNGYGEFGEGYVRI 365
           +GL ++G E       FY +A V +  N TE +  + ++  +  TPG  +G  GE ++RI
Sbjct: 300 DGLNKMGLECKKPDGAFYAFANVSDYGNGTEVAEKLLKEAHVAVTPGIAFGSSGEDFIRI 359

Query: 366 ALTVTEERIKEALERLK 382
           +   + +RI+EAL+RL+
Sbjct: 360 SYATSIDRIREALDRLE 376


Lambda     K      H
   0.316    0.139    0.414 

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: 417
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: 389
Length of database: 380
Length adjustment: 30
Effective length of query: 359
Effective length of database: 350
Effective search space:   125650
Effective search space used:   125650
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.

Links

Downloads

Related tools

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