GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Pontibacter ramchanderi LP43

Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate WP_101444119.1 BD749_RS09430 shikimate dehydrogenase

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



>NCBI__GCF_002846395.1:WP_101444119.1
          Length = 245

 Score =  232 bits (592), Expect = 5e-66
 Identities = 125/248 (50%), Positives = 163/248 (65%), Gaps = 8/248 (3%)

Query: 1   MEKYGLIGYPLRHSFSIGYFNEKFRSEGI-NAEYVNFEIPNINDFMEVIEENPNLCGLNV 59
           M ++GLIG  L HSFS  YF+EKF  EGI +A Y  +E+P I +F +++   P L GLNV
Sbjct: 1   MRRFGLIGKKLGHSFSKRYFSEKFAQEGIADAAYELYELPEIAEFPKLLAREPELVGLNV 60

Query: 60  TIPYKEQVIPFLNELDRDTAKIGAVNVIKIIRQPKGKVKLVGYNSDIIGFTQSIQPLLQP 119
           T+PYKE VIP+L+ELD   A+IGAVN I+I  +     +  GYN+D IGF  ++     P
Sbjct: 61  TVPYKELVIPYLHELDESAARIGAVNTIRIEGE-----RTKGYNTDYIGFRDTLLQFCPP 115

Query: 120 QHK-KALILGTGGASKAVYHGLKNLGIESVFVSRTHKTDDMLTYEELTPEIMEEYTVIVN 178
           +   KAL+LGTGGA+KAV+  L  L I    VSR + T + L YE +T E+++ Y++I+N
Sbjct: 116 EEGVKALVLGTGGAAKAVWATLDELAIPYTSVSR-NPTQNQLHYEAITTEVLQAYSLIIN 174

Query: 179 CTPVGMYPKVDFCPNIPYELLTPNHLLYDLLYNPNVTLFMKKGEAQGAVTKNGLEMLLLQ 238
            TP+GM P     P IPYE LT  H LYDL+YNP  TLF++KG   GA T NGL ML  Q
Sbjct: 175 TTPLGMAPNTAAAPAIPYEALTAGHYLYDLVYNPEETLFLQKGRLAGAHTINGLPMLYAQ 234

Query: 239 AFAAWEIW 246
           A AAW+IW
Sbjct: 235 ADAAWKIW 242


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: 220
Number of extensions: 13
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: 248
Length of database: 245
Length adjustment: 24
Effective length of query: 224
Effective length of database: 221
Effective search space:    49504
Effective search space used:    49504
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.

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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