GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Pseudomonas fluorescens FW300-N2E3

Align shikimate dehydrogenase (EC 1.1.1.25); quinate/shikimate dehydrogenase (EC 1.1.1.282) (characterized)
to candidate AO353_19825 AO353_19825 shikimate dehydrogenase

Query= BRENDA::Q88GF6
         (273 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_19825
          Length = 272

 Score =  378 bits (970), Expect = e-110
 Identities = 190/272 (69%), Positives = 220/272 (80%)

Query: 1   MPTTPSRDTVLCISLAGRPGTFGVRFHNHLYQQLGLDFYYKAMRTDDLPAAVAGIRALGI 60
           M   P++DT LC+SL+GRPG FG+RFHNHLY+QLGL+FYYKA  + DLP A+ GIRALGI
Sbjct: 1   MLMNPNKDTQLCMSLSGRPGNFGLRFHNHLYEQLGLNFYYKAFSSQDLPGAIGGIRALGI 60

Query: 61  RGCGVSMPYKEACMALVDEIDPSAAAIESVNTLVNCNGHLKAYNTDYLAVRQLLAQHQVD 120
           RGCGVSMP+KEAC+ALVDE+D SA AI S+NT+VN NG LKAYNTDY+A+ QLL  H V 
Sbjct: 61  RGCGVSMPFKEACIALVDELDASAQAIASINTIVNTNGRLKAYNTDYIAIEQLLKTHAVP 120

Query: 121 PGTAFALRGSGGMAKAVASALRDAGFAEGIIVARNEQAGRQLADVCGYRWVPEPGDICPP 180
             + FALRGSGGMAKAVASALRD G+  G+IVARNE AGR LAD  GYRW  E G   P 
Sbjct: 121 QDSTFALRGSGGMAKAVASALRDGGYQNGLIVARNESAGRALADSLGYRWQAELGSERPR 180

Query: 181 MLVNVTPIGMAGGLEAEELAFPEHAIAAAERVFDVVAMPAQTPLIRRAQALGKPVITGLE 240
           MLVNVTPIGM+GG EA++LAF   AI  AE VFDVVA+P++TPLI  A+A GK VITGLE
Sbjct: 181 MLVNVTPIGMSGGAEADQLAFDADAIDYAETVFDVVAIPSETPLIVHARAAGKRVITGLE 240

Query: 241 VIALQALEQFVLYTGVRPTREQVDAAVAYARA 272
           VIA+QALEQFVLYTGVRP+ EQ   AVA+AR+
Sbjct: 241 VIAIQALEQFVLYTGVRPSDEQFHKAVAFARS 272


Lambda     K      H
   0.322    0.136    0.406 

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: 315
Number of extensions: 5
Number of successful extensions: 1
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: 273
Length of database: 272
Length adjustment: 25
Effective length of query: 248
Effective length of database: 247
Effective search space:    61256
Effective search space used:    61256
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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