GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Ruegeria conchae TW15

Align acetylornithine aminotransferase; EC 2.6.1.11 (characterized)
to candidate WP_010441020.1 G7G_RS0109975 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= CharProtDB::CH_124889
         (441 letters)



>NCBI__GCF_000192475.1:WP_010441020.1
          Length = 1021

 Score =  120 bits (302), Expect = 2e-31
 Identities = 110/372 (29%), Positives = 168/372 (45%), Gaps = 45/372 (12%)

Query: 44  GANIISVYARYPVVAAKGEGSYLFDKEGRKYIDFTSGVAVTSLGHAHPEVARLAADQCSK 103
           G N+   Y   PV+  +G   +LFD+ GR Y+D  + V    +GHAHP +  +AADQ  +
Sbjct: 588 GGNLSLTYDD-PVMLVRGWKHHLFDEWGRPYLDAYNNVP--HVGHAHPRIQAVAADQLKR 644

Query: 104 LVHSSNLFYNEPA-IELSNVINNSLAKNSGIAGPTKIFFANCGTEANETALKFARKAAFE 162
           +  +SN  Y  PA    ++ I + L  +  +      FF N GTEANE AL+ AR     
Sbjct: 645 M--NSNTRYLHPAQTAFADKILSKLPDHLEVC-----FFVNSGTEANELALRLARAHT-- 695

Query: 163 KYGEGKSQIVYFNNSFHGRSLGSLSITA----NPK----------------YKRGFQPLL 202
               G   IV  ++ +HG +  +++I+A     P+                Y+  F+   
Sbjct: 696 ----GAKGIVTPDHGYHGNTNAAVAISAYKFNKPRGVGQADWVELVEVANDYRGSFRRDD 751

Query: 203 PDVVQAVYN--DPASIE--QFVNDKTAAVIVEPVQGEGGICPAKPEFLIALRKACDKVGA 258
           PD  +   +  DPA IE  Q      A  I E     GG       +L A+ +     G 
Sbjct: 752 PDRARRFADLVDPA-IEALQAKGHGLAGFIAETFPSVGGQIIPPKGYLPAVYEKIRAAGG 810

Query: 259 SLIYDEIQCGLGRSGDLWAHSIVKDVASPDIITVAKPLANGLPIGATIVSSKIAAEIHPG 318
             I DE+Q GLGR G+ +        A PDI+ + KP+ NG P+G  + + +IA     G
Sbjct: 811 VCIADEVQTGLGRLGEHY-FGFEHQGALPDIVVMGKPIGNGHPLGVLVTTKEIAQSFDNG 869

Query: 319 -EHGSTFGGNPVACRVGTFCVNELGSSKILQNVRKQHKALTSRFDDFVAKYPNLIRGYAG 377
            E  STFGG+ ++CR+G   ++ +    + +N R     L        A +   +    G
Sbjct: 870 IEFFSTFGGSTLSCRIGKEVLDIVDDEGLQENARVMGARLMDGLRQIEADFA-CVGDVRG 928

Query: 378 RGLLLGLQFTEP 389
            GL LG++   P
Sbjct: 929 MGLFLGVELINP 940


Lambda     K      H
   0.318    0.135    0.391 

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: 882
Number of extensions: 56
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: 441
Length of database: 1021
Length adjustment: 38
Effective length of query: 403
Effective length of database: 983
Effective search space:   396149
Effective search space used:   396149
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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