GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Desulfitobacterium hafniense DCB-2

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_015944380.1 DHAF_RS15445 diaminopimelate aminotransferase

Query= BRENDA::D2Z0I0
         (402 letters)



>NCBI__GCF_000021925.1:WP_015944380.1
          Length = 388

 Score =  305 bits (780), Expect = 2e-87
 Identities = 152/386 (39%), Positives = 238/386 (61%), Gaps = 6/386 (1%)

Query: 9   KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYS 68
           ++  L   VF  +++L+ +L + G+ +++L +G+PD  PS  I   L E       +GY+
Sbjct: 5   RLSSLGASVFTEMDDLRKELEKAGKQLINLSIGSPDRSPSAEIRKVLAEGVLDGGSYGYT 64

Query: 69  ASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPT 128
            ++G    R     +YK R+GV LDPE+  +  +G+++G +H+ LA+ +PGD  ++P+P 
Sbjct: 65  LTRGTESFRSGCARWYKERFGVNLDPEKEVLPLMGSQDGLAHIFLALCDPGDVALIPDPG 124

Query: 129 YPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTLC 188
           YPI+    ++ GG+ +++P+  E  F    L  L  +     ++ K + L++P+NPT   
Sbjct: 125 YPIYTAGLVLAGGEKVALPLREENGF----LPDLSAIEDEVAQQAKIMFLNYPNNPTAAV 180

Query: 189 VDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKGFS 248
             L FF+EVV  A++  I + HD AY++L FDGY P S LQV GA +V +E +S+SK ++
Sbjct: 181 APLSFFEEVVDFARRNRIVVCHDAAYSELAFDGYRPVSFLQVPGAKEVGIEFHSVSKTYN 240

Query: 249 MAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRRR 308
           +AG R+ F VGN  +I  LA LKS +DYGVF P   A   AL +  E VE+NR  Y+ RR
Sbjct: 241 LAGVRLGFAVGNGEIIGALAELKSNIDYGVFEPALQAGAYALSASQENVEQNRRAYQERR 300

Query: 309 DVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEYG 368
           D+ V+G  + GW +  P+GSMF+WA VP     +S  F+  L REA V V PG+ FGEYG
Sbjct: 301 DIWVKGCAQAGWSMPSPRGSMFIWAPVP--TAQDSRSFAFALAREAGVIVVPGVAFGEYG 358

Query: 369 EGYVRFALVENEHRIRQAVRGIKKAL 394
           EGYVR  +V+++  +++AVR +++ L
Sbjct: 359 EGYVRIGMVQDQEVLQEAVRRVQEFL 384


Lambda     K      H
   0.322    0.141    0.425 

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: 405
Number of extensions: 23
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: 402
Length of database: 388
Length adjustment: 31
Effective length of query: 371
Effective length of database: 357
Effective search space:   132447
Effective search space used:   132447
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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