GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Echinicola vietnamensis KMM 6221, DSM 17526

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate Echvi_0124 Echvi_0124 Aspartate/tyrosine/aromatic aminotransferase

Query= curated2:Q30ZX9
         (388 letters)



>FitnessBrowser__Cola:Echvi_0124
          Length = 386

 Score =  293 bits (749), Expect = 7e-84
 Identities = 151/381 (39%), Positives = 225/381 (59%), Gaps = 3/381 (0%)

Query: 7   ADRLATLPPYLFAQIDKVKAEVAARGVDIISLGIGDPDMPTPDFVIEALKKAAEKPANHQ 66
           A RLA +  Y F++  +  A + A G  II++GIG PD+P    V EAL  ++ +P +H 
Sbjct: 5   AHRLANVKEYYFSKKLREVARLKAEGHPIINMGIGSPDLPPHPSVTEALNHSSAQPTSHG 64

Query: 67  YPSYTGMLAFRQEVANWYKRRYAVELDPKTEVLTLIGSKEGIAHFPTAFVNPGDLVLVCP 126
           Y SY G+ A R+ +A++Y++ YAV L P  E+L ++GSKE I H   A++NPGD VL+  
Sbjct: 65  YQSYQGIPALREAIASFYQKHYAVSLSPTDEILPMMGSKEAIMHISLAYLNPGDKVLIPN 124

Query: 127 PCYPVYAIASRFMGGVVQELPLLEENDFLPDLDAVDEATWEKARCIFVNYPNNPTAAMAP 186
           P YP Y+  +  +G       L EEN +LPD+  ++E      + +++NYP+ PT A A 
Sbjct: 125 PGYPTYSSVTELVGAKAVYYDLKEENQWLPDIGQLEELAQSGIKLMWINYPHMPTGANAS 184

Query: 187 RSFFEKLIGIARKHNVIVVHDAAYTEMYYNENNRPLSIMEIPGAMDVAIEFNSLSKPYNM 246
           R   E L+  A+KH +++V+D  Y+   +     P+SI+ I GA D+A+E NSLSK +NM
Sbjct: 185 REALEALVTFAKKHQILLVNDNPYS---FILTQSPISILSIDGAKDIALELNSLSKTFNM 241

Query: 247 TGWRIAMAVGNASLVAGLGKVKENMDSGAFQAVQEAAIVALRDGDAFLAEIRDIYRKRRD 306
            GWR+ M  G AS +  + KVK NMDSG F  +QE AI AL     +  ++  IY KRR+
Sbjct: 242 PGWRVGMLCGQASYLQEVLKVKSNMDSGMFLGIQEGAIAALNLDQRWFDQMDAIYHKRRE 301

Query: 307 TVIAALNKIGITCRVPEASLYVWARVPEGYTSSDFVTRVLQETGVVMTPGNGFGAAGEGY 366
            V     ++G  C    A ++VWA++    T S  V ++L E  + +TPG+ FG+ G GY
Sbjct: 302 AVWKLAERVGAICERNSAGMFVWAKLATQTTPSALVDKLLYENHIFITPGDIFGSNGHGY 361

Query: 367 FRISLTVNDERLEEAVSRIAS 387
            R SL V +  ++EA  R+ S
Sbjct: 362 IRFSLCVPENLIQEAFDRVNS 382


Lambda     K      H
   0.320    0.136    0.403 

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: 418
Number of extensions: 16
Number of successful extensions: 2
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: 388
Length of database: 386
Length adjustment: 30
Effective length of query: 358
Effective length of database: 356
Effective search space:   127448
Effective search space used:   127448
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