GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Bacteroides thetaiotaomicron VPI-5482

Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate 353460 BT3934 putative phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase (NCBI ptt file)

Query= reanno::Pedo557:CA265_RS11635
         (379 letters)



>FitnessBrowser__Btheta:353460
          Length = 353

 Score =  377 bits (968), Expect = e-109
 Identities = 181/342 (52%), Positives = 248/342 (72%), Gaps = 5/342 (1%)

Query: 20  PLIISGPCSAETEEQLLTTAHLLAATGKVSVLRAGIWKPRTRPGEFEGIGSIGLEWLKRA 79
           P++I+GPCSAETEEQ++ TA  LAA G+  + RAGIWKPRT+PG FEGIG  GL WLK  
Sbjct: 16  PIVIAGPCSAETEEQVMETAKQLAAKGQ-KIYRAGIWKPRTKPGGFEGIGVEGLAWLKEV 74

Query: 80  KAETGLPTAVEVANAKHVEEALAAGVDILWIGARSTVNPFTVQEIADALKGHDVPVLIKN 139
           K ETG+  + EVA AKHV E L AG+DILW+GAR+T NPF VQEIADALKG D+PVL+KN
Sbjct: 75  KKETGMYVSTEVATAKHVYECLKAGIDILWVGARTTANPFAVQEIADALKGVDIPVLVKN 134

Query: 140 PVNPDLQLWIGAIERINGAGITKIGAIHRGFSSFEKSSFRNEPMWELAIQLKTLCPELPI 199
           PVNPDL+LWIGA+ERI+ AG+ ++GAIHRGFSS++K  +RN P W + I+L+   P LPI
Sbjct: 135 PVNPDLELWIGALERIHNAGLKRLGAIHRGFSSYDKKIYRNLPQWHIPIELRRRLPNLPI 194

Query: 200 INDPSHICGNRELIPYISQKALDLDMQGLMIESHVDPSVAWTDAKQQVTPAALAELVDRL 259
             DPSHI G REL+  + Q+A+DL+  GL++ESH +P  AW+DA QQVTP  L  +++ L
Sbjct: 195 FCDPSHIGGKRELVAPLCQQAMDLNFDGLIVESHCNPDCAWSDASQQVTPDVLDYILNLL 254

Query: 260 TVREPEAPNEAFADKLADLRKSIDKIDDVLLQKLGERMAIVEKIGEFKRDNQVTILQVNR 319
            +R      E+    L+ LRK ID+ DD ++Q+L +RM +  +IG +K+++ +T+LQ  R
Sbjct: 255 VIRTETQTTES----LSQLRKQIDECDDNIIQELAKRMRVAREIGTYKKEHGITVLQAGR 310

Query: 320 WDAIIKKGHAFAKALKLDLNFTEKFLELVHGESIRKQTEIMN 361
           ++ I++K  A  +   +  +F +   E +H ES+R+Q EI+N
Sbjct: 311 YNEILEKRGAQGEQCGMSADFMKLIFEAIHEESVRQQIEIIN 352


Lambda     K      H
   0.317    0.134    0.389 

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: 363
Number of extensions: 10
Number of successful extensions: 3
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: 379
Length of database: 353
Length adjustment: 30
Effective length of query: 349
Effective length of database: 323
Effective search space:   112727
Effective search space used:   112727
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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