GapMind for catabolism of small carbon sources

 

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

Align Fructose-bisphosphate aldolase class 1; Fructose-bisphosphate aldolase class I; FBP aldolase; EC 4.1.2.13 (characterized)
to candidate 351187 BT1659 fructose-bisphosphate aldolase class I (NCBI ptt file)

Query= SwissProt::P0A991
         (350 letters)



>FitnessBrowser__Btheta:351187
          Length = 350

 Score =  478 bits (1230), Expect = e-139
 Identities = 232/350 (66%), Positives = 283/350 (80%)

Query: 1   MTDIAQLLGKDADNLLQHRCMTIPSDQLYLPGHDYVDRVMIDNNRPPAVLRNMQTLYNTG 60
           M+ +  LLG      L H C TI    +Y+P  D +D+V ID++R   VL ++QTL   G
Sbjct: 1   MSKVVDLLGDKTSYYLDHTCKTIDKSLIYIPSPDTIDKVWIDSDRNIKVLNSLQTLLGHG 60

Query: 61  RLAGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGCNCVASTYGVLASVS 120
           RLA TGY+SILPVDQ +EH+AGASFA NP+YFDP+NIV+LAIE GCN VAST+G+L SV+
Sbjct: 61  RLANTGYVSILPVDQDIEHTAGASFAPNPIYFDPENIVKLAIEGGCNAVASTFGILGSVA 120

Query: 121 RRYAHRIPFLVKLNHNETLSYPNTYDQTLYASVEQAFNMGAVAVGATIYFGSEESRRQIE 180
           R+YAH+IPF+VKLNHNE L+YPNTYDQ L+ +V++A+NMGAVAVGATIYFGSE+SRRQ+ 
Sbjct: 121 RKYAHKIPFVVKLNHNELLTYPNTYDQVLFGTVKEAWNMGAVAVGATIYFGSEQSRRQLV 180

Query: 181 EISAAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQANHLAATIGADIVKQKM 240
           EI+ AFE AHELGM T+LW YLRNS FKK  +DYH +ADLTGQA+ L  TI ADIVKQK+
Sbjct: 181 EIAEAFEYAHELGMATILWCYLRNSDFKKGAIDYHAAADLTGQADRLGVTIKADIVKQKL 240

Query: 241 AENNGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAGLINSGGAAGGETDLS 300
             NNGG+KAI +G TD+R+Y++LTSE+PIDL RYQ+AN YMGR GLINSGG + G +DL 
Sbjct: 241 PTNNGGFKAIGFGKTDERMYTELTSEHPIDLCRYQVANGYMGRVGLINSGGESHGASDLR 300

Query: 301 DAVRTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVYLDSKITIA 350
           DAV TAV+NKRAGGMGLI GRKAF+K M  GV+L+NA+QDVYLD  ITIA
Sbjct: 301 DAVITAVVNKRAGGMGLISGRKAFQKPMNKGVELLNAIQDVYLDPAITIA 350


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: 439
Number of extensions: 13
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: 350
Length adjustment: 29
Effective length of query: 321
Effective length of database: 321
Effective search space:   103041
Effective search space used:   103041
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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