GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Xanthobacter autotrophicus Py2

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_011996059.1 XAUT_RS02030 pyridoxal phosphate-dependent aminotransferase

Query= curated2:B1I544
         (392 letters)



>NCBI__GCF_000017645.1:WP_011996059.1
          Length = 395

 Score =  204 bits (520), Expect = 3e-57
 Identities = 132/358 (36%), Positives = 178/358 (49%), Gaps = 6/358 (1%)

Query: 30  QGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYPSSAGMPAYRRAVADWYARRFGV 89
           QG  +++LGIG PD  TPDHI+EAA K L+    H Y  S G+   R AVA    RR+GV
Sbjct: 29  QGRSILNLGIGQPDFRTPDHIVEAAVKALR-DGQHGYTPSVGILPLREAVAADLNRRYGV 87

Query: 90  ELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPGYPVYAGGTILAGGIPHPVPLTA 149
           E+DP   V+ + G K  +      F +PG  +L PDPG+P+Y       G  P PVP+  
Sbjct: 88  EVDPDL-VMIMPGGKVTMYAAIRLFGEPGAEILYPDPGFPIYRSMIEHTGATPVPVPIRE 146

Query: 150 GNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVA-SKEFFARVVDFAREYGILVCHDAA 208
            NGF        A    + +++ IN P NPTG V  + E    V   A    + +  D  
Sbjct: 147 ENGFAFSAEETLALITPKTRLLIINSPANPTGGVTPAAEIDKLVKGLAAHPHVALMSDEI 206

Query: 209 YSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMTGWRAGWAAGNAGAVEALGRLKSN 268
           Y    FDG    + L     R+  I  +  SKTY MTGWR G++       + + +L  N
Sbjct: 207 YDRFLFDGEEHRTLLAYPQIRDRLILLNGWSKTYAMTGWRLGYSIWPKDLYDKVRKLAVN 266

Query: 269 LDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLVVDTLNDL-GWRLTRPRATFYIW 327
             S V    QYA IAAL GPQD V ++   +  RR +VVD LN L G R   P+  FY +
Sbjct: 267 CWSCVNAATQYAGIAALEGPQDAVDAMTAEFDARRRIVVDGLNALPGVRCATPKGAFYAF 326

Query: 328 APV--PAGHDASSFAEMVLEKAGVVITPGTGYGTYGEGYFRISLTLPTPRLVEAMERL 383
             V      +A   A  +LE+AGV +  G  +G YGEGY R+S       +  A+ R+
Sbjct: 327 PNVSGTGWSEAKKLASALLEEAGVAVIGGPDFGVYGEGYLRLSYATSRENIAAALARM 384


Lambda     K      H
   0.321    0.139    0.430 

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: 331
Number of extensions: 13
Number of successful extensions: 5
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: 392
Length of database: 395
Length adjustment: 31
Effective length of query: 361
Effective length of database: 364
Effective search space:   131404
Effective search space used:   131404
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 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