GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Desulfatibacillum aliphaticivorans DSM 15576

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_028314264.1 G491_RS0108285 alanine transaminase

Query= BRENDA::D2Z0I0
         (402 letters)



>NCBI__GCF_000429905.1:WP_028314264.1
          Length = 388

 Score =  456 bits (1174), Expect = e-133
 Identities = 220/389 (56%), Positives = 286/389 (73%), Gaps = 5/389 (1%)

Query: 7   FPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHG 66
           F ++ +LP YVFA VNE+K + RR GEDI+DLGMGNPD+   QHI+DK+ E A +P+ H 
Sbjct: 4   FARLDRLPPYVFAQVNEIKMEARRAGEDIIDLGMGNPDLGTPQHIVDKMVEAAQKPHNHR 63

Query: 67  YSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPN 126
           YSAS GI +LR AI D+YKRRY V++D E  AI+TIGAKEG SHL+L  + PGD V  P+
Sbjct: 64  YSASMGIRKLRMAIADWYKRRYDVDIDYENEAIVTIGAKEGISHLVLVTIRPGDVVFSPS 123

Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTT 186
           PTYPIH ++ II GGD   +P+ P+ DF E     L    + ++ KPK +VLSFPHNPT 
Sbjct: 124 PTYPIHPFSAIIAGGDVRQIPLGPDTDFFE----NLITATRQTWPKPKMMVLSFPHNPTG 179

Query: 187 LCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKG 246
             +DLEFF ++V+ AK+  I +VHDFAYADL +DGY  PS LQ  GA DV VE +S+SK 
Sbjct: 180 EVIDLEFFTKIVEFAKEHDIMVVHDFAYADLTYDGYKAPSFLQAPGAKDVGVEFFSLSKS 239

Query: 247 FSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRR 306
           +SMAGWRV F VGN  ++  L  +KSYLDYG+F PIQ+A+IIAL    E VE+ R+ Y+ 
Sbjct: 240 YSMAGWRVGFCVGNPKIVAALRRIKSYLDYGIFQPIQIAAIIALNGEQECVEEIRQTYKM 299

Query: 307 RRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEV-GMNSLDFSLFLLREAKVAVSPGIGFG 365
           RRD L +GL ++GW+V  PKG+MFVWAK+PE+   M S++FS  L++EAKVAV+PG+GFG
Sbjct: 300 RRDTLCDGLAKMGWDVPPPKGTMFVWAKIPEQYRSMGSVEFSKMLVKEAKVAVAPGLGFG 359

Query: 366 EYGEGYVRFALVENEHRIRQAVRGIKKAL 394
            YG+ YVRFAL+EN+ R +QA+RGI+  L
Sbjct: 360 HYGDDYVRFALIENKMRTQQALRGIRNVL 388


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: 512
Number of extensions: 18
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