GapMind for Amino acid biosynthesis

 

Alignments for a candidate for fbp in Echinicola vietnamensis KMM 6221, DSM 17526

Align Fructose-bisphosphate aldolase class 1; Fructose-bisphosphate aldolase class I; FBP aldolase; EC 4.1.2.13 (characterized)
to candidate Echvi_3158 Echvi_3158 DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes

Query= SwissProt::P0A991
         (350 letters)



>FitnessBrowser__Cola:Echvi_3158
          Length = 353

 Score =  447 bits (1149), Expect = e-130
 Identities = 214/348 (61%), Positives = 271/348 (77%)

Query: 3   DIAQLLGKDADNLLQHRCMTIPSDQLYLPGHDYVDRVMIDNNRPPAVLRNMQTLYNTGRL 62
           +I +LLG+ A   L+H C  I  D+L  P  + +D+V  ++NR P VLR++  LYN G L
Sbjct: 6   NIVELLGEKASFYLEHICEKITKDELQTPSKNSIDKVFGNSNRNPQVLRSLSQLYNHGNL 65

Query: 63  AGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGCNCVASTYGVLASVSRR 122
           AGTGYLSILPVDQG+EHSA  SF  NP YFDP+NI++LA+EAGCN VAST+GVL   +R+
Sbjct: 66  AGTGYLSILPVDQGIEHSAAYSFYKNPDYFDPENIIKLALEAGCNGVASTFGVLGLNARK 125

Query: 123 YAHRIPFLVKLNHNETLSYPNTYDQTLYASVEQAFNMGAVAVGATIYFGSEESRRQIEEI 182
           YAH+IPF+VK+NHNE L+YPN YDQTL+  V+ A++MGA+AVGATIYFGS ES RQ++EI
Sbjct: 126 YAHKIPFIVKINHNELLTYPNKYDQTLFGKVKTAWDMGAIAVGATIYFGSAESNRQLKEI 185

Query: 183 SAAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQANHLAATIGADIVKQKMAE 242
           + AFE AH LGM T+LW Y RN AFK +  DYH +AD+TGQANHL  TI ADI+KQK+  
Sbjct: 186 AEAFEEAHNLGMATILWCYTRNEAFKTEKEDYHAAADVTGQANHLGVTIQADIIKQKLPT 245

Query: 243 NNGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAGLINSGGAAGGETDLSDA 302
           NN G+K I +G  DD +Y  LT+++PIDL R Q+ANCYMG+ GLINSGG + GE+DL +A
Sbjct: 246 NNFGFKEIGFGKYDDEMYKTLTTDHPIDLCRLQVANCYMGKIGLINSGGGSKGESDLVEA 305

Query: 303 VRTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVYLDSKITIA 350
           + TAVINKRAGG GLI+GRKAF+K   +G++L+  VQDVYLD KI+IA
Sbjct: 306 ITTAVINKRAGGSGLIMGRKAFQKPFTEGIELLRFVQDVYLDQKISIA 353


Lambda     K      H
   0.318    0.134    0.386 

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: 400
Number of extensions: 9
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: 350
Length of database: 353
Length adjustment: 29
Effective length of query: 321
Effective length of database: 324
Effective search space:   104004
Effective search space used:   104004
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 (21.7 bits)
S2: 49 (23.5 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