GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Paraburkholderia bryophila 376MFSha3.1

Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate H281DRAFT_06075 H281DRAFT_06075 3-isopropylmalate dehydratase, large subunit

Query= curated2:Q8TLF1
         (424 letters)



>FitnessBrowser__Burk376:H281DRAFT_06075
          Length = 469

 Score =  226 bits (576), Expect = 1e-63
 Identities = 154/441 (34%), Positives = 212/441 (48%), Gaps = 57/441 (12%)

Query: 38  VDYAMAHDGTSVLAVNAFKEMEMEKVWDPSRIVVPFDHIAPANNETSATLQREIREWVKE 97
           +D  + H+ TS  A    K +    VW  S  +   DH  P  + +        +  V  
Sbjct: 27  IDRHLLHEVTSPQAFEGLK-LAQRPVWRISANLAVSDHNVPTTDRSHGIADPVSKLQVDT 85

Query: 98  -------QGIPNFY--EVGEGICHQVLPENGFALPGKLVVGADSHSCTYGAFGAFATGVG 148
                   GI  F   ++ +GI H + PE G  LPG  +V  DSH+ T+GAFGA A G+G
Sbjct: 86  LDSNCDAYGITQFKMNDLRQGIVHIIGPEQGATLPGMTIVCGDSHTSTHGAFGALAHGIG 145

Query: 149 ATDMAEIFATGKLWFKVPESFRMTVEGSLRKGVYAKDLTLYLIGKTGIAGATYKAVEFYG 208
            +++  + AT  L  K  ++  + VEG L +G  AKD+ L +IGK G AG T  A+EF G
Sbjct: 146 TSEVEHVLATQTLLQKKSKNMLVKVEGPLPRGCTAKDIVLAIIGKIGTAGGTGYAIEFGG 205

Query: 209 QAIRELTVAGRMTLCNMAIEMGAKTGIVPPDEKTFEFLKNR-----------AAATYEPV 257
             IR L++ GRMT+CNMAIE GA+ G+V  D+ T E+LK R           A   ++  
Sbjct: 206 STIRSLSMEGRMTVCNMAIEAGARAGMVAVDDTTIEYLKGRPFSPQGAEWDHAVEYWKQF 265

Query: 258 YADPDAVYLEEFTYDADDIEPQV---ACPHQVDNV------------------------- 289
            +D  A +      +A DI PQV     P  V  V                         
Sbjct: 266 KSDEGAQFDRVVELNAADIVPQVTWGTSPEMVTAVDGRVPDPEREKDPVKRDAMERALKY 325

Query: 290 ---KPVGEVEGTHVDQVFIGTCTNGRLEDLEVAAAVLK--GKQVAVR---TIVIPASRTT 341
              +P   +E    D++FIG+CTN R+ED+  AA V+K  G++VA      +V+P S   
Sbjct: 326 MALEPNAPIESIKPDKIFIGSCTNARIEDIRAAAYVVKKLGRRVAPNIRLAMVVPGSGLV 385

Query: 342 LLAAIENGTMETLLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKGGFI 401
              A   G  +    AG     PGC  CL  +   L  GE C ST+NRNF+GR G GG  
Sbjct: 386 KAQAEREGLDKVFTDAGFEWREPGCSMCLAMNADRLDPGERCASTSNRNFEGRQGAGGRT 445

Query: 402 YLASPATAAASALTGEITDPR 422
           +L SPA AAA+A+ G   D R
Sbjct: 446 HLVSPAMAAAAAIEGHFVDIR 466


Lambda     K      H
   0.318    0.135    0.400 

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: 483
Number of extensions: 19
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 424
Length of database: 469
Length adjustment: 32
Effective length of query: 392
Effective length of database: 437
Effective search space:   171304
Effective search space used:   171304
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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