GapMind for Amino acid biosynthesis

 

Alignments for a candidate for fbp in Paucidesulfovibrio gracilis DSM 16080

Align fructose-1,6-bisphosphate aldolase subunit (EC 4.1.2.13) (characterized)
to candidate WP_078717302.1 B5D49_RS08675 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase

Query= metacyc::MONOMER-11810
         (281 letters)



>NCBI__GCF_900167125.1:WP_078717302.1
          Length = 270

 Score =  166 bits (421), Expect = 4e-46
 Identities = 95/264 (35%), Positives = 151/264 (57%), Gaps = 13/264 (4%)

Query: 12  RLKRFFRRD-GRALIFAMDHGFEHGPTDFEPVWEHVNPRVIIRKVVRAGIDGVMMLPGLA 70
           R++R   RD GR ++  +DHG   GP     ++  V+ R  + KV   G + V+M  GL 
Sbjct: 8   RMERIMNRDNGRLIVVPLDHGVTVGP-----IYGLVDLRDTVNKVADGGANAVLMHKGLP 62

Query: 71  RIAGDEVKPEVGLMIKLTSKTNLRPKPEQLLQSQLGFVDDAIKLGADAIAATVYWGSPQE 130
           R +      ++GL++ L++ T L P P    ++ +G V+DAIKLGADA++  V  G   E
Sbjct: 63  RCSHRGTGRDIGLIVHLSASTALSPTPNA--KTMVGTVEDAIKLGADAVSIHVNLGDESE 120

Query: 131 DVMMRQFAEIVSYAHDLGYPVVQFAYPRGPYIDEKYGKKEDYRVVMYGARAAAESGADMI 190
             M+     + S A D G PV+   Y RGP + ++Y       VV + AR   E GAD++
Sbjct: 121 RSMLSDLGALCSRAGDWGMPVLAMLYARGPKVKDEYAPD----VVAHCARVGMELGADIV 176

Query: 191 KTYWTGSKETFAKVVEAAAGVPVLLSGGAKTENPVDFLKVVWEVIEAGGAGAVVGRNIFQ 250
           K  +TG  E+F +V E    VPV+++GG K ++  D +++V + ++AGGAG  VGRNIFQ
Sbjct: 177 KVNYTGDPESFQRVTEGCC-VPVVIAGGPKVDSNYDLVRMVHDSVQAGGAGISVGRNIFQ 235

Query: 251 RENPEPMIKALIRVIHRNEDPEEA 274
            ++P  ++++L +V+H     E+A
Sbjct: 236 HDHPARLVRSLYKVVHEGWSVEQA 259


Lambda     K      H
   0.320    0.138    0.409 

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: 196
Number of extensions: 10
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: 281
Length of database: 270
Length adjustment: 25
Effective length of query: 256
Effective length of database: 245
Effective search space:    62720
Effective search space used:    62720
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: 47 (22.7 bits)

This GapMind analysis is from Jul 25 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