GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Rhizorhabdus wittichii RW1

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_012050345.1 SWIT_RS21085 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P18335
         (406 letters)



>NCBI__GCF_000016765.1:WP_012050345.1
          Length = 434

 Score =  239 bits (610), Expect = 1e-67
 Identities = 142/411 (34%), Positives = 217/411 (52%), Gaps = 35/411 (8%)

Query: 24  AEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS-NVFT 82
           A     + + + IWD +G+ Y+DFA GIAV  +GH HP ++ A++ Q     H +  V  
Sbjct: 28  APIFAARAENAEIWDVEGRRYIDFASGIAVLNVGHRHPRIIAAVEEQLGRFTHTAFQVVG 87

Query: 83  NEPALRLGRKL---IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHN 139
            EP +RL  +L          + +F  +G EA E A K+AR+      +  ++ +IAF N
Sbjct: 88  YEPYVRLAERLNALAPVVGPAKTIFFTTGAEATENAVKIARY------ASGRSAVIAFVN 141

Query: 140 AFHGRSLFTVSVGGQP-KYSDGFGPKPADIIHVPF----------NDLHAVKAVMDD--- 185
            FHGR+L   ++ G+   Y  GFGP P DI H+PF          + L A+  V+     
Sbjct: 142 GFHGRTLLASAMTGKVLPYKKGFGPLPGDIYHIPFPSEAHGITVEHSLAALANVLSSDVE 201

Query: 186 --HTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMH 243
             +  A+++EP+QGEGG   A  EFL+ LR LCD+H   L+ DEVQ G+GRTG LFA  H
Sbjct: 202 AANVAAIILEPVQGEGGFHVAPFEFLRALRSLCDEHGIALIADEVQTGIGRTGKLFAVEH 261

Query: 244 YGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIIN 303
            GV PD++T AK+LGGGFP+SA++  A +     PG  G TY G+P+ACA   A  D+I 
Sbjct: 262 AGVRPDLITVAKSLGGGFPLSAVVGNAALIDRVPPGGLGGTYAGSPIACAAGLAVLDVIE 321

Query: 304 TPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDI-RGMGLLIGAELKPQYK------GRARD 356
              + +  +   +R  + L  +  + ++   + RG+G +I  +++            A+ 
Sbjct: 322 QDRLCDRAERMGRRITERLSAVAARRELPIGLPRGLGAMIAFDIRAGLDDLRPDGAAAKR 381

Query: 357 FLYAGAEAGVMVLNAGP--DVMRFAPSLVVEDADIDEGMQRFAHAVAKVVG 405
                 E G+++L  G   + +R    L   DA +DEG+   A A+A  +G
Sbjct: 382 VCVRALELGLILLTCGQHGEAIRLLAPLTASDAVLDEGLDILAQALADTLG 432


Lambda     K      H
   0.322    0.138    0.415 

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: 476
Number of extensions: 19
Number of successful extensions: 7
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: 434
Length adjustment: 32
Effective length of query: 374
Effective length of database: 402
Effective search space:   150348
Effective search space used:   150348
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 (21.9 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