GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Dyella japonica UNC79MFTsu3.2

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase

Query= SwissProt::P18335
         (406 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3308
          Length = 411

 Score =  372 bits (956), Expect = e-108
 Identities = 191/391 (48%), Positives = 256/391 (65%), Gaps = 3/391 (0%)

Query: 18  LPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHI 77
           LP+Y P E +   G+G+R+WD +G++YVD   GIAV ALGH  P LV+AL TQ   LWH 
Sbjct: 19  LPVYRPREVVLDHGKGARVWDTEGRDYVDLGAGIAVNALGHQDPDLVDALVTQARKLWHS 78

Query: 78  SNVFTNEPALRLGRKLIEAT-FAERVVFMNSGTEANETAFKLARHYACVR-HSPFKTKII 135
           SNVF  EP L L  +L++A+ FAERV   NSGTEANE A KL R +A  +  +P +  I+
Sbjct: 79  SNVFYTEPPLHLAEELVQASGFAERVFLCNSGTEANEAAIKLVRKWAASKGRAPEQRVIL 138

Query: 136 AFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVM-DDHTCAVVVEP 194
            F  +FHGR+L  V+   QPKY + + P P    ++ FND+  ++A        AV++EP
Sbjct: 139 TFRGSFHGRTLAAVTATAQPKYQENYEPLPGGFRYLDFNDVAGLEAAFAQGDVAAVMLEP 198

Query: 195 IQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSA 254
           +QGEGGV  A+P F++  RELCD H+ALLV DE+QCGMGRTG LFA+   GVTPDI+T A
Sbjct: 199 VQGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMGRTGTLFAHAQDGVTPDIVTLA 258

Query: 255 KALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEGIQAK 314
           KALG GFPI AML   ++A     G+HG+T+GGNP+A AVA  A   + + E++  +  +
Sbjct: 259 KALGCGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALRKLASAELMANVAKQ 318

Query: 315 RQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYAGAEAGVMVLNAGPD 374
            Q   D L  ID +  +F+++RG GL++GA L   YKGRA + L   A  G++VL AGPD
Sbjct: 319 AQALRDGLAAIDGELKLFAEVRGRGLMLGAVLAEAYKGRAGEVLDHAAAHGLLVLQAGPD 378

Query: 375 VMRFAPSLVVEDADIDEGMQRFAHAVAKVVG 405
           V+RF P L + DAD+ EG+ R   A+A  VG
Sbjct: 379 VLRFVPPLNITDADLAEGLARLRAALADFVG 409


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: 488
Number of extensions: 20
Number of successful extensions: 4
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: 411
Length adjustment: 31
Effective length of query: 375
Effective length of database: 380
Effective search space:   142500
Effective search space used:   142500
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