GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Desulfovibrio vulgaris Miyazaki F

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate 8500663 DvMF_1411 aminotransferase class I and II (RefSeq)

Query= BRENDA::Q2RK33
         (390 letters)



>FitnessBrowser__Miya:8500663
          Length = 394

 Score =  355 bits (911), Expect = e-102
 Identities = 163/388 (42%), Positives = 253/388 (65%), Gaps = 3/388 (0%)

Query: 1   MQEARRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPE 60
           M +  R+  LPPY+FA + +   + R + VDI+ LG+G+PD+PTP H++DKLV  +    
Sbjct: 1   MNQFPRMHRLPPYVFATVNELKMQLRRQNVDIVDLGMGNPDIPTPQHIVDKLVEASGKGV 60

Query: 61  NHRYPTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINL 120
           NHRY  S G+   R+A+ DWY R +GV LDP  E V  +G+KEG++H+SL  + PGD+  
Sbjct: 61  NHRYSVSRGIPNLRKAICDWYMRRFGVYLDPDTEAVATMGAKEGLSHLSLAMLSPGDVVF 120

Query: 121 VPDPGYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGA 180
            PDP YP++    ++AG +   +P+     F  DL         + KL+FI+YP+NPT  
Sbjct: 121 APDPTYPIHTYAPIIAGADVRRIPIGRGRDFFEDLLVATRQTWPQPKLLFISYPHNPTCE 180

Query: 181 VADLKFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPY 240
           +A  +FFQ+VV+FA+ + + V HD AY+++ +DG+  PSF+QA GAK+VG+EF S+SK Y
Sbjct: 181 IAAPEFFQKVVDFAKEHKIYVIHDFAYADLAFDGHMPPSFMQAEGAKDVGVEFFSMSKSY 240

Query: 241 NMTGWRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQER 300
           +M GWR+G+  G  D++ AL RIKS +D G FQ +Q A   AL GPQE + E+   Y++R
Sbjct: 241 SMAGWRVGFCVGNRDLVYALTRIKSYLDYGHFQPIQIAATVALNGPQECVTEIVDTYRKR 300

Query: 301 RDIIVEGFNSLGWHLEKPKATFYVWAPVP---RGYTSASFAEMVLEKAGVIITPGNGYGN 357
           RD+++EG    GW +  PK T +VWA +P   R   S  F++++L++  V ++PG G+G 
Sbjct: 301 RDVLIEGLGRAGWVVPPPKGTMFVWAQIPEEFRAMGSVEFSKLLLKEGHVAVSPGLGFGA 360

Query: 358 YGEGYFRIALTISKERMQEAIERLRRVL 385
           +G+ + R AL  ++ R ++A++ +++VL
Sbjct: 361 HGDDHVRFALIENEHRTKQAMKGIKKVL 388


Lambda     K      H
   0.320    0.139    0.421 

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: 451
Number of extensions: 22
Number of successful extensions: 1
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: 390
Length of database: 394
Length adjustment: 31
Effective length of query: 359
Effective length of database: 363
Effective search space:   130317
Effective search space used:   130317
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 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