GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Cupriavidus basilensis 4G11

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate RR42_RS26240 RR42_RS26240 4-aminobutyrate aminotransferase

Query= SwissProt::P18335
         (406 letters)



>FitnessBrowser__Cup4G11:RR42_RS26240
          Length = 420

 Score =  247 bits (630), Expect = 5e-70
 Identities = 149/397 (37%), Positives = 214/397 (53%), Gaps = 38/397 (9%)

Query: 26  FIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS-NVFTNE 84
           F   + + S +WD +G  Y+DFA GIAV   GH HP LV A++ Q E   H +  +    
Sbjct: 24  FYAERAENSELWDVEGNRYIDFAAGIAVLNTGHRHPRLVQAMQAQMERFTHTAYQIVPYA 83

Query: 85  PALRLGRKL---IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAF 141
             + L  K+       FA++  F  +G EA E A K+AR       +  +  +IAF   F
Sbjct: 84  SYIELAEKINARAPGAFAKKTAFFTTGAEAVENAIKIARA------ATGRPGVIAFSGGF 137

Query: 142 HGRSLFTVSVGGQP-KYSDGFGPKPADIIHVPF-------------NDLHAV-KAVMDD- 185
           HGR++  +++ G+   Y  GFGP P D+ H P+             N LH + KA +D  
Sbjct: 138 HGRTMMGMALTGKVVPYKVGFGPFPGDVFHAPYPYGLHGVSVQDSINALHQLFKADVDPK 197

Query: 186 HTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYG 245
              A++ EP+QGEGG   A  EF++ LR +CD+H  LLV DEVQ G GRTG LFA  HY 
Sbjct: 198 RVAAIIFEPVQGEGGFNVAPAEFVRALRAICDEHGILLVADEVQTGFGRTGKLFAMEHYD 257

Query: 246 VTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTP 305
           VTPD+ T AK+L GG P+SA+   AEI  A  PG  G TY GNPLA A A A  D++ + 
Sbjct: 258 VTPDLTTMAKSLAGGMPLSAVCGRAEIMDAPAPGGLGGTYAGNPLAVASALAVLDVLESE 317

Query: 306 EVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELK-------PQYKGRARDFL 358
           +++E   A  QR  D L  +  +     ++RG+G +I  E +       P++  + +D  
Sbjct: 318 KLIERGAALGQRLQDKLDGLKSRVPEIGEVRGVGAMIAVEFRKADGRPDPEFTRQVQD-- 375

Query: 359 YAGAEAGVMVLNAG--PDVMRFAPSLVVEDADIDEGM 393
               E G+++L+ G   +V+RF   L + DA +DEG+
Sbjct: 376 -RALERGLLLLSCGVYGNVVRFLFPLTIPDAVMDEGL 411


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: 474
Number of extensions: 29
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: 406
Length of database: 420
Length adjustment: 31
Effective length of query: 375
Effective length of database: 389
Effective search space:   145875
Effective search space used:   145875
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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