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_06175 AO353_06175 shikimate dehydrogenase

Query= BRENDA::Q88K85
         (282 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_06175
          Length = 284

 Score =  424 bits (1090), Expect = e-123
 Identities = 216/281 (76%), Positives = 239/281 (85%), Gaps = 1/281 (0%)

Query: 1   MSQQ-AILAGLIGRGIQLSRTPALHEHEGDAQALRYLYRLIDADQLQLDDSALPGLLEAA 59
           MSQ   +LAGLIG GIQ SRTPALHE EGDAQ LRYLYRLID DQL+LD  ALP LL +A
Sbjct: 1   MSQNNTVLAGLIGAGIQASRTPALHEREGDAQGLRYLYRLIDLDQLKLDSGALPDLLMSA 60

Query: 60  QHTGFTGLNITYPFKQAILPLLDELSDEARGIGAVNTVVLKDGKRVGHNTDCLGFAEGLR 119
           +   FTGLNIT+P KQAI+PLLDELS EARGIGAVNTVVLKDGKR+GHNTDCLGFAEG R
Sbjct: 61  ERMNFTGLNITFPCKQAIIPLLDELSPEARGIGAVNTVVLKDGKRIGHNTDCLGFAEGFR 120

Query: 120 RGLPDVARRQVVQMGAGGAGSAVAHALLGEGVERLVLFEVDATRAQALVDNLNTHFGAER 179
           RGL D AR +VVQMGAGGAG+AVAHALL EGV++L +F+VD +RAQ+L +NLN HFG+ R
Sbjct: 121 RGLKDAARERVVQMGAGGAGAAVAHALLSEGVQQLSIFDVDVSRAQSLANNLNQHFGSGR 180

Query: 180 AVLGTDLATALAEADGLVNTTPVGMAKLPGTPLPVELLHPRLWVAEIIYFPLETELLRAA 239
           A  G+DL +ALA+ADGLVNTTP+GMAKLPG P+PVELL   LWVAEI+YFPLETELLR A
Sbjct: 181 ACAGSDLPSALAQADGLVNTTPMGMAKLPGMPVPVELLRAELWVAEIVYFPLETELLRNA 240

Query: 240 RALGCRTLDGSNMAVFQAVKAFELFSGRQADAARMQAHFAS 280
           RALGCRTLDG NMAVFQAVKAFELFSG   DA RM AHF S
Sbjct: 241 RALGCRTLDGGNMAVFQAVKAFELFSGVAPDAQRMLAHFQS 281


Lambda     K      H
   0.321    0.137    0.395 

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: 288
Number of extensions: 3
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: 282
Length of database: 284
Length adjustment: 26
Effective length of query: 256
Effective length of database: 258
Effective search space:    66048
Effective search space used:    66048
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.

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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