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_066329653.1 BLR17_RS09610 aspartate aminotransferase family protein

Query= reanno::Cola:Echvi_3848
         (381 letters)



>NCBI__GCF_900100165.1:WP_066329653.1
          Length = 398

 Score =  155 bits (393), Expect = 1e-42
 Identities = 126/384 (32%), Positives = 185/384 (48%), Gaps = 32/384 (8%)

Query: 17  ASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNIAF------YSNSVQIP 70
           A GS I+D    +YLD   G +  ++GH  P   + IK+QLD  +       YS S  + 
Sbjct: 24  AIGSYIYDTNNKKYLDFVAGVSACTLGHQPPRVNQAIKDQLDKYSHVMVYGEYSQSPAVE 83

Query: 71  IQKELATKLGQLSGYPDYDLFLCNSGAEANENALKLASFETGKKGFIAFTKGFHGRTSGA 130
             K +A+ L +    P    +L NSG EA E +LKLA   TG+  +I+    +HG T G+
Sbjct: 84  YCKLMASLLPE----PLNKTYLVNSGTEAIEGSLKLARRVTGRSQWISCYNAYHGNTMGS 139

Query: 131 VALTDNPKIIAPFNAH-EGVHILPFNDLEAVEKQLATGTIAGVIVEGIQGVGGIQVPDPA 189
           +++    +    F      V  + FN+   +EK   T   AGV++E IQG  G   P   
Sbjct: 140 MSVMGFEERKQAFRPLIPDVDFITFNNEADLEK--ITTKTAGVLLETIQGGAGFIEPQND 197

Query: 190 FLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVEGLKPDLITVAKGMGNGFPIGGV 249
           +L  +     + GA LILDE+Q G+ R+GK F  Q  + + PD++ + KGMG G P+G  
Sbjct: 198 YLKKVRERCTEVGAMLILDEIQPGFGRTGKLFGFQNYD-IVPDIVAMGKGMGGGMPVGAF 256

Query: 250 LISP---EFKASHGLLG--TTFGGNHLACAAALAVLEVIDEENLITAAAENGKAIMAALE 304
             S    +    +  LG  TTFGG+ +  AA LA L+ I E +L+  A E  K   + L 
Sbjct: 257 TASSAMMDLLTENPKLGHITTFGGHPVIAAACLATLKEITETDLMQEALEKEKLFRSLLV 316

Query: 305 KVAGVTEVRGKGLMIGFDLATEAGPVRAALIHEHK-------IFTGSAGGKHTIRLLPPL 357
               + EVRGKGLM+    AT        L  + K       +F G A     IR+ PPL
Sbjct: 317 HPL-IQEVRGKGLMLAAMTATAEITNEVILKCQDKGLILFWLLFEGCA-----IRITPPL 370

Query: 358 NIEPKALTLFLEKLETVLNVKQST 381
            I  + +      + TV++  Q +
Sbjct: 371 TISNEEIREGCNIMLTVMDEIQKS 394


Lambda     K      H
   0.318    0.137    0.400 

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: 378
Number of extensions: 28
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: 381
Length of database: 398
Length adjustment: 30
Effective length of query: 351
Effective length of database: 368
Effective search space:   129168
Effective search space used:   129168
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: 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