GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Flavobacterium glycines Gm-149

Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate WP_066329651.1 BLR17_RS09620 shikimate dehydrogenase

Query= reanno::Btheta:353741
         (248 letters)



>NCBI__GCF_900100165.1:WP_066329651.1
          Length = 249

 Score =  254 bits (650), Expect = 9e-73
 Identities = 127/248 (51%), Positives = 173/248 (69%), Gaps = 6/248 (2%)

Query: 2   EKYGLIGYPLRHSFSIGYFNEKFRSEGI-NAEYVNFEIPNINDFMEVIEENPNLCGLNVT 60
           +++GL+G  + +SFS G+F  KF  E + N  Y NF+I  I+ F E+I+   +L GLNVT
Sbjct: 7   KRFGLLGRNISYSFSKGHFTTKFEKEKLQNYTYENFDIQEISAFPEIIKNTDHLSGLNVT 66

Query: 61  IPYKEQVIPFLNELDRDTAKIGAVNVIKIIRQPKGKVKLVGYNSDIIGFTQSIQPLLQPQ 120
           IPYKE VIP+L++L +   KIGAVN IK  +  KGK+K  GYN+D  GF +S++PLL+P 
Sbjct: 67  IPYKEDVIPYLDKLSKKAKKIGAVNTIKFTK--KGKLK--GYNTDYFGFLKSLEPLLKPH 122

Query: 121 HKKALILGTGGASKAVYHGLKNLGIESVFVSRTHKTDDMLTYEELTPEIMEEYTVIVNCT 180
           HKKALILGTGGASK V   L+ LGIE +FVSR   ++  + Y ++  E  +EY +I+N T
Sbjct: 123 HKKALILGTGGASKGVAFALEELGIEYLFVSRK-ASEKAIDYSQINTETFKEYQIIINST 181

Query: 181 PVGMYPKVDFCPNIPYELLTPNHLLYDLLYNPNVTLFMKKGEAQGAVTKNGLEMLLLQAF 240
           P+G  P ++ CP IPYEL T  H+ YDL+YNP  T F+K  +A+GA  KNGL+ML+ QA 
Sbjct: 182 PIGTSPNIEACPEIPYELFTDKHIAYDLIYNPAETQFLKNAKARGAQIKNGLDMLIFQAE 241

Query: 241 AAWEIWHR 248
            AWEIW++
Sbjct: 242 KAWEIWNK 249


Lambda     K      H
   0.320    0.140    0.419 

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: 236
Number of extensions: 10
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: 248
Length of database: 249
Length adjustment: 24
Effective length of query: 224
Effective length of database: 225
Effective search space:    50400
Effective search space used:    50400
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 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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