GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Clostridium acetobutylicum ATCC 824

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_014518834.1 CA_RS02090 aspartate aminotransferase family protein

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>NCBI__GCF_000008765.1:WP_014518834.1
          Length = 426

 Score =  228 bits (580), Expect = 3e-64
 Identities = 141/409 (34%), Positives = 218/409 (53%), Gaps = 42/409 (10%)

Query: 26  VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNGYTN-EPVL 84
           VRGEG+ L+ + G++ +DFA G+AV  LGH +P ++KA  EQ  K  H G+     E  +
Sbjct: 25  VRGEGAYLYTEDGRKVLDFASGVAVCNLGHNNPAVIKAAKEQMDKLIHGGHNVVYYESYV 84

Query: 85  RLAKQLIDATF-ADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTL 143
           +LA+++++ T     V+F NSGAEANE A+KLA+      + +++  I++FK +FHGRTL
Sbjct: 85  KLAEKIVELTGNKTMVYFSNSGAEANEGAIKLAK------YITKRQAIISFKGSFHGRTL 138

Query: 144 FTVS-AGGQPAYSQDFAPLPPQIQHAIYNDL---------------------DSAKALID 181
            T S  G    Y +++  L P +  A Y                        D  K LI+
Sbjct: 139 ATTSITGSSSKYRKNYEGLLPSVYFAEYPYCFRCPYKQNKESCNMECISQFEDMFKKLIE 198

Query: 182 -DNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMH 240
            ++  A+I+EP+QGEGG +     FL+ +RE+CD +   LIFDEVQ G GRTG+++A+ +
Sbjct: 199 PESVAAIIMEPVQGEGGYIVPPKKFLKAVREICDKYGICLIFDEVQCGFGRTGKIFAHEN 258

Query: 241 YGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATIN 300
           + V PD+ + AKA+  GFP+ A++  +        G HG T+GGNP+ACA +    ATI 
Sbjct: 259 FEVEPDIFTCAKAIASGFPLSAVIGKKELMEKWPAGAHGGTFGGNPVACAAS---LATIK 315

Query: 301 TRE--VLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIG---CVLKDEYAGKAKAIS 355
             E  VL+       +  E L  +  +Y    +IRG+GL+IG   C   +   G      
Sbjct: 316 ELESGVLDNANNMGNYLKEELLKLKDKYACIGDIRGIGLMIGMEFCKENNNPDGDIVTFI 375

Query: 356 NQAAEEGLMILIAGA---NVVRFAPALIISEDEVNSGLDRFELACKRFL 401
            + A    +IL+      NV+RF   L + + E++  +   E     +L
Sbjct: 376 REVAVNNNLILLGCGTEHNVLRFIAPLTVEKSEIDMAISIVEKGIVEYL 424


Lambda     K      H
   0.321    0.137    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: 463
Number of extensions: 21
Number of successful extensions: 5
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: 406
Length of database: 426
Length adjustment: 31
Effective length of query: 375
Effective length of database: 395
Effective search space:   148125
Effective search space used:   148125
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 25 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