GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Pontibacter ramchanderi LP43

Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_101442815.1 BD749_RS02630 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= reanno::Btheta:353284
         (373 letters)



>NCBI__GCF_002846395.1:WP_101442815.1
          Length = 383

 Score =  453 bits (1165), Expect = e-132
 Identities = 223/376 (59%), Positives = 286/376 (76%), Gaps = 3/376 (0%)

Query: 1   MKLFDVYPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATL 60
           M LFDVYPL+DI  V+  G  VWD+ G +YLDLYGGHAVISIGH+HPHYV+ I+ Q+  +
Sbjct: 1   MNLFDVYPLFDIEPVRAAGLSVWDKEGRKYLDLYGGHAVISIGHSHPHYVKRIARQLYDI 60

Query: 61  GFYSNSVINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFS 120
           GFYSN+V   +QQ++A +LGK+SGY+ YS FL NSGAEANENALKLASF  GR KVISFS
Sbjct: 61  GFYSNAVQMPMQQELAVKLGKLSGYDAYSFFLCNSGAEANENALKLASFQTGRKKVISFS 120

Query: 121 KAFHGRTSLAVEATNNPTIIAPINNNGHVTYLPLNDIEAMKQELAKG--DVCAVIIEGIQ 178
            +FHGRTS AV AT++ +I+APIN   ++ ++P ND+ A ++ L K   ++ AVI+EGIQ
Sbjct: 121 ASFHGRTSAAVAATDDTSIVAPINQTDNIIFMPFNDVAAFEEALQKHGQELAAVIVEGIQ 180

Query: 179 GVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKG 238
           GVGG+ IPT  F++ L   C + G +LILDE+QSGYGRSGKFFAHQ+  IQPD+ITVAKG
Sbjct: 181 GVGGVNIPTVNFLKALEAGCKKVGALLILDEVQSGYGRSGKFFAHQHAGIQPDLITVAKG 240

Query: 239 IGNGFPMAGVLISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYL 298
           +GNGFP+ GVLISP  +  +G LGTTFGGN+LAC+A+LAV++VIE++ L+ENA  +G YL
Sbjct: 241 MGNGFPVGGVLISPEIEARHGMLGTTFGGNYLACAASLAVLEVIEKEELLENATIMGHYL 300

Query: 299 LEELKKFPQIKEVRGRGLMIGLEFEEPIKELRSRLIYDEHVFTGASGT-NVLRLLPPLCL 357
            E+L+  P +KEVRG+GLMIG+E  EP   +R  L+    +FTG+S   N LRLLP L +
Sbjct: 301 KEQLEGMPGVKEVRGQGLMIGIELNEPCAGIRKELLSQFGIFTGSSSNKNTLRLLPALTI 360

Query: 358 SMEEADEFLARFKRVL 373
           S  EAD FL  F  +L
Sbjct: 361 SKAEADLFLKAFSSIL 376


Lambda     K      H
   0.320    0.139    0.403 

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: 411
Number of extensions: 16
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: 373
Length of database: 383
Length adjustment: 30
Effective length of query: 343
Effective length of database: 353
Effective search space:   121079
Effective search space used:   121079
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: 50 (23.9 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