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 8500823 DvMF_1564 aminotransferase class I and II (RefSeq)

Query= BRENDA::Q2RK33
         (390 letters)



>FitnessBrowser__Miya:8500823
          Length = 400

 Score =  157 bits (397), Expect = 5e-43
 Identities = 109/357 (30%), Positives = 170/357 (47%), Gaps = 8/357 (2%)

Query: 33  ISLGIGDPDMPTPSHVIDKLV-AEAHNPENHRYPTSEGLLAFRQAVADWYQRLYGVDLDP 91
           +SLG G P   TP H+++ +  A   +P   RY    G+ A R+A+A       G   DP
Sbjct: 39  VSLGQGVPSFRTPDHIVEAVCRALRDDPTAGRYSLQPGMPALREAIAADILARKGARFDP 98

Query: 92  RREVVTLIGSKEGIAHISLCYVDPGDINLVPDPGYPVYNIGTLLAGGESYFMPLTAANGF 151
             E+   +G+ E +  I L  V+ GD  ++P PGY  +    L+A G    +PL AA+  
Sbjct: 99  ETEIGVTVGAMEALVMIMLTVVERGDEVIIPSPGYASHAEQVLMAEGVPVHVPLRAADWG 158

Query: 152 LPDLGAIPSDVARRAKLMFINYPNNPTGAVADLKFFQEVVEFARSYDLIVCHDAAYSEIT 211
           L D+ A+   V  R + + +  P NPTG V D    + + + A   DL++  D  Y  + 
Sbjct: 159 L-DVEAVRFAVTPRTRAIIVCSPGNPTGGVYDDADVRALCDLALERDLVLIVDDTYDYMV 217

Query: 212 Y---DGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTGWRLGWACGRADVIEALARIKSNID 268
           Y    G    S +  P  +   I  NS SK Y +TGWR+G+    A  +  L ++     
Sbjct: 218 YGEQPGTPRFSPVSQPELRRHVITVNSFSKKYALTGWRVGYVAADAAWMAELLKVHDATA 277

Query: 269 SGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDIIVEGFNSLGWHLE--KPKATFYVWA 326
             A    Q+A +AALTGPQ+ +  +R     RRD+     ++L  H     P+  FY  A
Sbjct: 278 VCAPTVSQHAALAALTGPQDCVDVMRAALTARRDLTCRRLDALAPHFAYVPPRGAFYAMA 337

Query: 327 PVP-RGYTSASFAEMVLEKAGVIITPGNGYGNYGEGYFRIALTISKERMQEAIERLR 382
                   S + A  +LE+A VI  PG  +G  GE + R++  + +  + EA +R++
Sbjct: 338 RYTFTDADSMTVARRMLEEARVITVPGGSFGPTGERHLRLSFGMDEAELTEAFDRIQ 394


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: 388
Number of extensions: 19
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: 390
Length of database: 400
Length adjustment: 31
Effective length of query: 359
Effective length of database: 369
Effective search space:   132471
Effective search space used:   132471
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