GapMind for Amino acid biosynthesis

 

Aligments for a candidate for aroA in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS (uncharacterized)
to candidate Echvi_0122 Echvi_0122 5-enolpyruvylshikimate-3-phosphate synthase

Query= curated2:Q5LHG9
         (410 letters)



>lcl|FitnessBrowser__Cola:Echvi_0122 Echvi_0122
           5-enolpyruvylshikimate-3-phosphate synthase
          Length = 405

 Score =  316 bits (810), Expect = 7e-91
 Identities = 185/395 (46%), Positives = 249/395 (63%), Gaps = 11/395 (2%)

Query: 12  KATIQLPASKSISNRALIIHALSKGDDVPSNLSDCDDTQVMIKALTEGNEVIDILAAGTA 71
           + TI LP+SKS SNR LI+ AL++G +  SNL++  DTQ MI+ L E  E +D+L AGT 
Sbjct: 14  EVTIPLPSSKSESNRVLIVDALTEGQNQISNLAEARDTQTMIRLLAEDPETLDVLDAGTT 73

Query: 72  MRFLTAYLSSTPGIHTITGTERMQQRPIQILVNALRELGAHIEYVRNEGFPPLRIEG--R 129
           MRFLTAY + T    T+TGT RM +RPI ILV+ALR +GA IEY   EG+PP+   G  +
Sbjct: 74  MRFLTAYAALTNRRKTLTGTPRMCERPIGILVDALRAIGAKIEYKGKEGYPPMETLGFEK 133

Query: 130 ELTGSEITLKGNVSSQYISALLMIGPVLKNGLQLRLTGEIVSRPYINLTLQLMKDFGASA 189
           +LT +++ ++G+VSSQYISALLM  P+L  GL L LTG+I S+ YI +TL+LMK FG + 
Sbjct: 134 QLT-NKVQIRGDVSSQYISALLMNAPLLPEGLTLELTGKIGSKTYITMTLELMKQFGIAY 192

Query: 190 SWTSDQNIQVDPQPYHCLPFTVESDWSAASYWYQIAALSPQADIELTGLFRHSYQGDSRG 249
           S+  +  I + PQ Y    F VESDWS ASYW+ + A + +    L GL  +S QGDS+ 
Sbjct: 193 SFEGN-TISIAPQSYKNTSFAVESDWSGASYWFSLLACADEGSFFLKGLKENSLQGDSKI 251

Query: 250 AEVFARLGVATEYTETGIRLKKNGTCVERLDE-DFVDIPDLAQTFVVTCALLNVPFRFTG 308
            E+  +LGV +E+ + GI L K    +  L   DF   PDLAQT  VTCAL+    +FTG
Sbjct: 252 VEIMDKLGVQSEFKDDGILLTKK--AITGLGSYDFTHCPDLAQTVAVTCALIGQKSQFTG 309

Query: 309 LQSLKIKETDRIEALKTEMKKLGYILHD-KNDSILSWDGERVEQQTCPVIKTYEDHRMAM 367
           L+SL+IKETDRI AL+ E+ K    L + +N +        +       I+TY+DHRM M
Sbjct: 310 LESLRIKETDRIYALQQELAKFNAKLEEGENGAFTVIPSTDIPANV--TIETYDDHRMGM 367

Query: 368 AFAPAAIHYPTIQIDEPQVVSKSYPGYWDDLRKAG 402
           AF P         +D+ +VV+KSYP +W     AG
Sbjct: 368 AFMPLVTKTSVTLLDK-EVVNKSYPSFWKHCVLAG 401


Lambda     K      H
   0.318    0.135    0.394 

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: 394
Number of extensions: 18
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: 410
Length of database: 405
Length adjustment: 31
Effective length of query: 379
Effective length of database: 374
Effective search space:   141746
Effective search space used:   141746
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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