GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Azoarcus sp. BH72

Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate WP_011763948.1 AZO_RS01095 aspartate aminotransferase family protein

Query= SwissProt::Q940M2
         (476 letters)



>NCBI__GCF_000061505.1:WP_011763948.1
          Length = 460

 Score =  167 bits (423), Expect = 7e-46
 Identities = 130/406 (32%), Positives = 202/406 (49%), Gaps = 43/406 (10%)

Query: 88  YLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTIYLHHAIGDFAEALA 147
           +L D  G+  LDAFAG+  V+ G+ H  ++ A  EQ + L +AT  +   +  + A  LA
Sbjct: 40  WLRDIHGKEVLDAFAGLWCVNIGYGHESVVQAAAEQMRKLPYATGYFGFGS--EPAIRLA 97

Query: 148 AKM----PGNLKVVYFVNSGSEANELAMMMARLYTGSL------EMISLRNAYHGGSSNT 197
           AK+    P +L+  Y    GSEA + A+ +   Y  +         I++   YHG SS  
Sbjct: 98  AKLAEIAPKSLRHTYLTLGGSEAVDAAIRLITHYYNATGRPQKKHFIAIERGYHGSSSVG 157

Query: 198 IGLTALNTWK--YPLPQGEIHHVVNPDPYRGVFGSD---------GSLYAKDVHDHIEYG 246
            GLTAL  +   + +P    H++ +P PYR   G D          +L AK      E G
Sbjct: 158 SGLTALPAFHRGFDVPLPNQHYIASPYPYRSPVGDDPQAVIAASVAALRAKVA----ELG 213

Query: 247 TSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGF 306
               VA F  E +QG GG +    G+LK++ E  R  G + + DEV TGFGRTG  +   
Sbjct: 214 ADN-VAAFFCEPVQGSGGVIVPPKGWLKAMREASRELGILFVVDEVITGFGRTGPMF-AC 271

Query: 307 QTQDVVPDIVTMAKGIGNG-LPLGAVVTTPEIASVLASKILFN-------TFGGNPVCSA 358
             +DV PD++TMAKG+ +G +P+GA++ + E+ + +A     N       T+ G+PV +A
Sbjct: 272 LAEDVEPDLMTMAKGLTSGYVPMGALMISDEVYNGIADGAAPNVLVGHGATYSGHPVSAA 331

Query: 359 GGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDK 418
             L V+ + ++     H   +       L ++   H ++GDVR RGL+  +ELV+D+  K
Sbjct: 332 VALEVIRLYEEGGILAHAQAMEPGFAAGLGEMLD-HPLVGDVRHRGLLGAVELVADKASK 390

Query: 419 ---TPAKAETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDD 461
               PA      LF    + G++    G H  +    P +CFT+D+
Sbjct: 391 RAFDPALGLADRLFRSGYQNGLIFRSFGDH--ILGFAPALCFTEDN 434


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: 575
Number of extensions: 29
Number of successful extensions: 6
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: 460
Length adjustment: 33
Effective length of query: 443
Effective length of database: 427
Effective search space:   189161
Effective search space used:   189161
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