GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Sinorhizobium meliloti 1021

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate SMc01578 SMc01578 aspartate aminotransferase

Query= curated2:Q30ZX9
         (388 letters)



>FitnessBrowser__Smeli:SMc01578
          Length = 400

 Score =  174 bits (441), Expect = 4e-48
 Identities = 120/395 (30%), Positives = 191/395 (48%), Gaps = 21/395 (5%)

Query: 6   LADRLATLPPYLFAQIDKVKAEVAARGVDIISLGIGDPDMPTPDFVIEALKKAAEKPANH 65
           LAD L+ + P     + +   E+ A+G D+I LG G+PD  TPD + +A   A ++    
Sbjct: 4   LADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDR-GET 62

Query: 66  QYPSYTGMLAFRQEVANWYKRRYAVELDPKTEVLTLIGS--KEGIAHFPTAFVNPGDLVL 123
           +Y   +G+   R+ +A  +KR   ++    T   T++G+  K+ + +   A +NPGD V+
Sbjct: 63  KYTPVSGIPELREAIAKKFKRENNLDY---TAAQTIVGTGGKQILFNAFMATLNPGDEVV 119

Query: 124 VCPPCYPVYAIASRFMGGVVQELPLLEENDFLPDLDAVDEATWEKARCIFVNYPNNPTAA 183
           +  P +  Y       GG    +P  +EN+F    + +D A   K +    N P+NP+ A
Sbjct: 120 IPAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGA 179

Query: 184 MAPRSFFEKLIGIARKH-NVIVVHDAAYTEMYYNENNRPLSIMEIPGAMDVAIEFNSLSK 242
                  + L  +  KH +V V+ D  Y  + Y +      +   PG  +  +  N +SK
Sbjct: 180 AYSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSK 239

Query: 243 PYNMTGWRIAMAVGNASLVAGLGKVKENMDSGAFQAVQEAAIVALRDGDAFLAEIRDIYR 302
            Y MTGWRI  A G   L+  +  ++    SGA    Q AA+ AL     F+   ++I++
Sbjct: 240 AYAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQ 299

Query: 303 KRRDTVIAALNKI-GITCRVPEASLYVW--------ARVPEG---YTSSDFVTRVLQETG 350
            RRD V++ LN+  GI+C  PE + YV+           P G    T  DFV+ +L+  G
Sbjct: 300 GRRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEG 359

Query: 351 VVMTPGNGFGAAGEGYFRISLTVNDERLEEAVSRI 385
           V +  G+ FG      FRIS   ++  LEEA  RI
Sbjct: 360 VAVVHGSAFGLGPN--FRISYATSEALLEEACRRI 392


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: 382
Number of extensions: 25
Number of successful extensions: 6
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: 400
Length adjustment: 31
Effective length of query: 357
Effective length of database: 369
Effective search space:   131733
Effective search space used:   131733
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