GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Synechococcus elongatus PCC 7942

Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate Synpcc7942_2090 Synpcc7942_2090 homoserine dehydrogenase

Query= BRENDA::Q56R01
         (433 letters)



>FitnessBrowser__SynE:Synpcc7942_2090
          Length = 445

 Score =  325 bits (834), Expect = 1e-93
 Identities = 183/433 (42%), Positives = 271/433 (62%), Gaps = 15/433 (3%)

Query: 8   KVALLGCGVVGSEVARIMTTHGDDHAARIGAPVELAGVAVRRPSKVRA-GIPQELITTDA 66
           KV LLG G VG+  A+I+    D     +   +EL  V VR   K R+  I ++ +TTD 
Sbjct: 17  KVGLLGLGTVGTGTAQILLDPADRQP--LLQELELYRVGVRSLDKPRSVDISRDRLTTDL 74

Query: 67  TALVKRGDIDVVIEVIGGIEPARTLITTAFEHGASVVSANKALLAEDGATLYAAAERHGR 126
            ++V+   +D+V+E++GG+EP+R+LI TA  HG  VV+ANKA++A  G  ++AAA   G 
Sbjct: 75  ESIVRDPAVDIVVELLGGLEPSRSLILTAIAHGKHVVTANKAVIARYGEEIFAAAADAGV 134

Query: 127 DLYFEAAVAGAIPLIRPLRESSPGNKVNRVLGIVNGTTNFILDRMDSSGAGYTEALDEAT 186
            +  EAAV G IP+I PL++S   N++  +LGI+NGTTN+IL RM   G  +   L +A 
Sbjct: 135 YVLLEAAVGGGIPVIEPLKQSLCANRIQGILGIINGTTNYILTRMQREGGDFGPILADAQ 194

Query: 187 ALGYAEADPTADVEGFDAAAKAAILAGIAFHTRVRLDDVHREGLTEVTAADMASARRMGC 246
            LGYAEADPTADV+G+DAA K AILA +AF  RV    +  EG+  +TA+D+A A  +G 
Sbjct: 195 RLGYAEADPTADVDGWDAADKIAILASLAFGGRVERSQITCEGIRAITASDIAYAEGLGF 254

Query: 247 TVKLLAICERAADGRS--VTARVHPAMIPLSHPLASVREAYNAVFVESEAAGQLMFYGPG 304
           T+KLLA  +R   G +  + A V+P ++PLSHPLASV + YNA+ VE +  GQ+MF+GPG
Sbjct: 255 TIKLLAKAKRQHQGDTWRLEASVYPTLVPLSHPLASVNDVYNAILVEGDPVGQVMFFGPG 314

Query: 305 AGGAPTASAVLGDLVAVCRNKLAGATGPG-----ESAYTQ-LPVSPMGEVVTRYHISLDV 358
           AG  PTASAV+ D++ +     AG+            Y Q + ++P  E   R+++ + V
Sbjct: 315 AGAGPTASAVVADILNIAAVLSAGSDRDHLDPLLACRYLQTVELAPAAETAARFYLRIVV 374

Query: 359 ADKPGVLAQVATVFAEHGVSIDTVRQQGRQDSSGE-ASLVVVTHRAPDAALQGTVEALRS 417
            D PGV+ +V T+F E G+S++++ Q    D SGE A LVV+TH   +  ++  +  L +
Sbjct: 375 QDSPGVIGKVGTIFGEQGISLESIVQ---TDVSGETAELVVITHEVQEGIMRQAITQLEA 431

Query: 418 LDTVRGVASIMRV 430
           L  V+ +A+++ V
Sbjct: 432 LPLVQAIANLLHV 444


Lambda     K      H
   0.317    0.132    0.371 

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: 443
Number of extensions: 23
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: 433
Length of database: 445
Length adjustment: 32
Effective length of query: 401
Effective length of database: 413
Effective search space:   165613
Effective search space used:   165613
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