GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Dinoroseobacter shibae DFL-12

Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate 3606654 Dshi_0085 3-isopropylmalate dehydratase, large subunit (RefSeq)

Query= curated2:Q8TLF1
         (424 letters)



>FitnessBrowser__Dino:3606654
          Length = 467

 Score =  270 bits (689), Expect = 9e-77
 Identities = 172/463 (37%), Positives = 248/463 (53%), Gaps = 57/463 (12%)

Query: 14  TISEKIFSRAAGTEAKANDFVLADVDYAMAHDGTSVLAVNAFKEMEMEKVWDPSRIVVPF 73
           T+ +KI+      EA+    +L  +D  + H+ TS  A    + M    V  P + +   
Sbjct: 5   TLYDKIWDAHLAHEAEDGTCLLY-IDRHLVHEVTSPQAFEGLR-MAGRTVRAPDKTIAVP 62

Query: 74  DHIAPAN---------NETSATLQREIREWVKEQGIPNFYEVGE---GICHQVLPENGFA 121
           DH  P            E S      + +  K+ GI ++Y V +   GI H V PE G+ 
Sbjct: 63  DHNVPTTLGRENPDQMTEDSRIQVEALDKNAKDFGI-HYYPVSDIRQGIVHIVGPEQGWT 121

Query: 122 LPGKLVVGADSHSCTYGAFGAFATGVGATDMAEIFATGKLWFKVPESFRMTVEGSLRKGV 181
           LPG  VV  DSH+ T+GAFGA A G+G +++  + AT  L  K  ++ ++ + G LR GV
Sbjct: 122 LPGMTVVCGDSHTATHGAFGALAHGIGTSEVEHVLATQTLIQKKSKNMKVEITGKLRPGV 181

Query: 182 YAKDLTLYLIGKTGIAGATYKAVEFYGQAIRELTVAGRMTLCNMAIEMGAKTGIVPPDEK 241
            AKD+TL +IG TG AG T   +E+ G+AIR+L++ GRMT+CNMAIE GA+ G++ PDEK
Sbjct: 182 TAKDITLSVIGATGTAGGTGYVIEYCGEAIRDLSMEGRMTVCNMAIEGGARAGLIAPDEK 241

Query: 242 TFEFLKNR-----------AAATYEPVYADPDAVYLEEFTYDADDIEPQVACPHQVDNVK 290
           T+E+++ R           A A ++ +Y+D DA + +  T   +DI P V      ++V 
Sbjct: 242 TYEYVQGRPHAPKGAQWEAALAWWKTLYSDDDAHWDKVVTIKGEDIAPVVTWGTSPEDVL 301

Query: 291 PV------------GEVEGT------------------HVDQVFIGTCTNGRLEDLEVAA 320
           P+            G+V+                     +D VFIG+CTNGR+EDL  AA
Sbjct: 302 PISAMVPAPEDFTGGKVDAARRSLDYMGLTPGTPLSEIEIDTVFIGSCTNGRIEDLRAAA 361

Query: 321 AVLKGKQVAV-RTIVIPASRTTLLAAIENGTMETLLKAGVTLATPGCGPCLGAHQGVLGE 379
            +LKGK++AV R +V+P S      A E G  +   +AG      GC  CL  +   L E
Sbjct: 362 EILKGKKIAVKRAMVVPGSGLVRAQAEEEGLADIFKQAGFEWRMAGCSMCLAMNPDQLSE 421

Query: 380 GEVCVSTANRNFKGRMGKGGFIYLASPATAAASALTGEITDPR 422
           GE C ST+NRNF+GR G  G  +L SPA AAA+A+TG++TD R
Sbjct: 422 GERCASTSNRNFEGRQGYKGRTHLVSPAMAAAAAVTGKLTDVR 464


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: 545
Number of extensions: 20
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: 424
Length of database: 467
Length adjustment: 32
Effective length of query: 392
Effective length of database: 435
Effective search space:   170520
Effective search space used:   170520
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