GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Thiomicrorhabdus arctica DSM 13458

Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate WP_019557719.1 F612_RS0110440 aspartate aminotransferase family protein

Query= SwissProt::Q940M2
         (476 letters)



>NCBI__GCF_000381085.1:WP_019557719.1
          Length = 392

 Score =  172 bits (435), Expect = 2e-47
 Identities = 122/409 (29%), Positives = 196/409 (47%), Gaps = 42/409 (10%)

Query: 74  YYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTI 133
           Y + P+   +G    L D  G+ YLDA +GI   S GH HP I  AI +QS+ L H + +
Sbjct: 9   YARLPVTFEKGDGATLQDSEGKMYLDAISGIAVTSLGHAHPFISEAICKQSQQLIHTSNL 68

Query: 134 YLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLY-----TGSLEMISLRN 188
           Y        A+ L       ++ V+F NSG+EANE A+ +A+ +       +  ++ + N
Sbjct: 69  YHIKKQQMLADQLIEL--SGMEQVFFCNSGAEANEAAIKIAKKFGHQQGITNPTIVVMEN 126

Query: 189 AYHGGSSNTIGLTALNTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDHIE---- 244
           ++HG +  T+  T                  NP  + G     G  + +   D++     
Sbjct: 127 SFHGRTMATLSATG-----------------NPKVHEGFQPLVGG-FTRVPFDNVAAVEA 168

Query: 245 YGTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYW 304
              +  +   + E IQG GG      GYLK++ +I      + + DE+QTG GRTG  ++
Sbjct: 169 LSDNRDIVAILVEPIQGEGGVYVPQKGYLKALRKICDANNWLLMIDEIQTGMGRTGQ-WF 227

Query: 305 GFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAGGLAVL 364
            FQ +++ PD++T+AK +GNG+P+GA +   +   VLA      TFGGNP+  A GLAV+
Sbjct: 228 AFQHENITPDVLTLAKALGNGVPIGACIANNKATDVLAPGNHGTTFGGNPLACAVGLAVI 287

Query: 365 NVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKAE 424
            V+         A+ G+ L+ + K    +   I  +RG+G M+GI+L     D+  A+  
Sbjct: 288 EVLKTHNYIPAIAKKGALLLNQFKSALTQQPGISSIRGQGYMIGIQL-----DRPCAE-- 340

Query: 425 TSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVDALDYSI 473
              L +   E G+L+      G+  R+ P    ++   D LV  L   I
Sbjct: 341 ---LVKMALERGLLINV--TRGDTVRLLPSFVMSQQQTDELVTKLSQLI 384


Lambda     K      H
   0.320    0.138    0.412 

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: 401
Number of extensions: 11
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: 476
Length of database: 392
Length adjustment: 32
Effective length of query: 444
Effective length of database: 360
Effective search space:   159840
Effective search space used:   159840
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 (21.8 bits)
S2: 51 (24.3 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