GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Flavobacterium glycines Gm-149

Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_066329149.1 BLR17_RS14830 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

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



>NCBI__GCF_900100165.1:WP_066329149.1
          Length = 379

 Score =  440 bits (1132), Expect = e-128
 Identities = 215/374 (57%), Positives = 274/374 (73%), Gaps = 1/374 (0%)

Query: 1   MKLFDVYPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATL 60
           M LFDVYPLY I  VK   C ++DE GTEYLDLY GH VISIGH  P YV  +  Q+  L
Sbjct: 1   MNLFDVYPLYPITPVKAVDCTIYDEKGTEYLDLYSGHGVISIGHTQPDYVAKVKEQLDNL 60

Query: 61  GFYSNSVINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFS 120
            FYSN++ N LQ ++AE+LGK SG  D+SLFL +SGAEANENALKLASF+  +++VI+F 
Sbjct: 61  SFYSNAIQNPLQVELAEKLGKASGLTDFSLFLCSSGAEANENALKLASFHTNKSRVIAFD 120

Query: 121 KAFHGRTSLAVEATNNPTIIAPINNNGHVTYLPLNDIEAMKQELAKGDVCAVIIEGIQGV 180
            +FHGRTS AV  T+N  I+AP+N    VT+LPLN IE ++ EL KGDVCAVIIE IQGV
Sbjct: 121 NSFHGRTSAAVAVTDNKKIVAPLNAQQEVTFLPLNQIELVEAELKKGDVCAVIIEPIQGV 180

Query: 181 GGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKGIG 240
           GG+   TTEF Q L K       ILILDE+QSGYGRSGKFFA Q++ I PDI+T AKG+G
Sbjct: 181 GGLDQGTTEFFQALEKASKANDVILILDEVQSGYGRSGKFFAFQHHGINPDIVTTAKGMG 240

Query: 241 NGFPMAGVLISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYLLE 300
           NGFP+ GVLISP F+  YG LGTTFGG+HLAC+A +AV+DV+E   L+EN   V +Y  E
Sbjct: 241 NGFPIGGVLISPKFQASYGLLGTTFGGSHLACAAGIAVLDVMEDKKLIENTNKVSEYFFE 300

Query: 301 ELKKFPQIKEVRGRGLMIGLEFEEPIKELRSRLIYDEHVFT-GASGTNVLRLLPPLCLSM 359
            +K  P+IK+V+GRGLM+G+EF+  +  LR ++I ++++FT GA+  N+LR+LPPL ++ 
Sbjct: 301 AIKVIPEIKKVKGRGLMLGVEFDFDVSALRKKMIIEKYIFTGGANNKNLLRILPPLTITT 360

Query: 360 EEADEFLARFKRVL 373
           E  D F+   +  L
Sbjct: 361 EAIDTFIVALQESL 374


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: 427
Number of extensions: 19
Number of successful extensions: 2
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: 379
Length adjustment: 30
Effective length of query: 343
Effective length of database: 349
Effective search space:   119707
Effective search space used:   119707
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