GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Hafnia paralvei ATCC 29927

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_008814762.1 M988_RS18375 class II fructose-bisphosphate aldolase

Query= BRENDA::I3EBM6
         (285 letters)



>NCBI__GCF_001655005.1:WP_008814762.1
          Length = 287

 Score =  233 bits (595), Expect = 3e-66
 Identities = 129/287 (44%), Positives = 175/287 (60%), Gaps = 5/287 (1%)

Query: 1   MPLVSMTEMLNKAKAEGYAVGQFNLNNLEFTQAILLAAEEEKSPVILGVSEGAGRYMGGF 60
           MP VS   M+ +A   GYA+G F+ +N E  +AILLAA+EE+SPV++ V +     MG  
Sbjct: 1   MPYVSGKTMIQQAWKHGYAIGAFSAHNAETVRAILLAAQEEQSPVMIQVGQKVISVMG-L 59

Query: 61  KTVVNMVKGLMEDYKITVPVAIHLDHGSSFEKCKEVIDAGFTSVMIDASHHPFEENVEVT 120
           K +  ++   M D  ITVPV IHLDH  SFE+  + I  GF SVM D SH  FEENV +T
Sbjct: 60  KPMKEIIDAFMHD--ITVPVCIHLDHSRSFEQTMQAIQCGFQSVMFDGSHLSFEENVRIT 117

Query: 121 KKVVEYAHARGVSVEAELGTVGGQEDDVIAD--GVIYADPKECEELVKRTGIDCLAPALG 178
           +   E AHA  + +E E+G +GG EDD+  D    +     E     + T +D LA ++G
Sbjct: 118 RAASEVAHALNIGMEGEIGKIGGTEDDISVDEKDALITSCDEALRFSEGTDVDYLAVSIG 177

Query: 179 SVHGPYKGEPNLGFKEMEEIGRITGVPLVLHGGTGIPTKDIQRAISLGTAKINVNTENQI 238
           + HG YK EP L F  ++EI  I   P+VLHGG+G+P   I++AI+LG AK+NV+TE + 
Sbjct: 178 TAHGVYKQEPKLAFGRLQEIREIVKKPIVLHGGSGVPDDQIRQAIALGVAKVNVDTELRQ 237

Query: 239 ASAKKVREVLAENPNMYDPRKYLGPARDAIKETVIGKMREFGSSGKA 285
           A  + + EVL  +P  Y     LG  RD +KE VI K+R FGS+GKA
Sbjct: 238 AFTQGLCEVLTNDPEEYALAVSLGHGRDVMKEKVIEKIRLFGSNGKA 284


Lambda     K      H
   0.314    0.134    0.379 

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: 242
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: 285
Length of database: 287
Length adjustment: 26
Effective length of query: 259
Effective length of database: 261
Effective search space:    67599
Effective search space used:    67599
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: 42 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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