GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuB in Bacteroides thetaiotaomicron VPI-5482

Align 3-isopropylmalate/3-methylmalate dehydrogenase; 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; IPMDH; Beta-IPM dehydrogenase; D-malate dehydrogenase [decarboxylating]; EC 1.1.1.85; EC 1.1.1.n5; EC 1.1.1.83 (characterized)
to candidate 351599 BT2071 isocitrate dehydrogenase [NADP] (NCBI ptt file)

Query= SwissProt::Q58130
         (333 letters)



>lcl|FitnessBrowser__Btheta:351599 BT2071 isocitrate dehydrogenase
           [NADP] (NCBI ptt file)
          Length = 396

 Score =  174 bits (441), Expect = 3e-48
 Identities = 128/378 (33%), Positives = 183/378 (48%), Gaps = 56/378 (14%)

Query: 7   IEGDGIGKEVVPATIQVLEATGLP-------FEFVYAEAGDEVYKRTGKALPEETI---- 55
           I GDG+G EV P+   V+ A            E+    AG+  +  TG  LP+ET+    
Sbjct: 23  ITGDGVGAEVTPSMQSVVNAAVQKAYGGKRRIEWKEVLAGERAFNETGSWLPDETMKAFQ 82

Query: 56  ETALDCDAVLFGAAGETAADVIVKLRHILDTYANIRPVKAYKGVKC---LRPDIDYVIVR 112
           E  +     L    G     + V LR  LD Y  +RPV+ Y+GV         ++  + R
Sbjct: 83  EYLIGIKGPLTTPVGGGIRSLNVALRQTLDLYVCLRPVRWYQGVHSPVKAPEKVNMCVFR 142

Query: 113 ENTEGLYKGIEAEI--------------DEGIT---------IATRVITEKACERIFRFA 149
           ENTE +Y GIE E               + G+T            + ++ +  ER+ R A
Sbjct: 143 ENTEDIYAGIEWEAGTPEAEKFYQFLKNEMGVTKVRFPETSSFGVKPVSREGTERLVRAA 202

Query: 150 FNLARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVAE-EYDDIKAE------DYYI 202
              A +         VT  HK N++K T+G FKK  Y++A+ E+ D  A+      D   
Sbjct: 203 CQYALDHHLPS----VTLVHKGNIMKFTEGGFKKWGYELAQREFGDALADGRLVIKDCIA 258

Query: 203 DAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSANIGDE--HGLFEPVHG 260
           DA     +  P+ + V+ T NL GD +SD  A  VGG+G+AP ANI  +  H +FE  HG
Sbjct: 259 DAFLQNTLLIPEEYSVIATLNLNGDYVSDQLAAMVGGIGIAPGANINYKTGHAIFEATHG 318

Query: 261 SAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLALGLTTPDL------G 314
           +AP+IAGK + NP + ILSAV+ML YLG  EAA  +EKALE+       T DL      G
Sbjct: 319 TAPNIAGKDVVNPCSIILSAVMMLEYLGWKEAAALIEKALEQSFLDARATHDLARFMPGG 378

Query: 315 GNLNTFEMAEEVAKRVRE 332
            +L+T     E+ +R+ +
Sbjct: 379 TSLSTTAFTREIVERIEK 396


Lambda     K      H
   0.318    0.138    0.390 

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: 302
Number of extensions: 19
Number of successful extensions: 7
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: 333
Length of database: 396
Length adjustment: 29
Effective length of query: 304
Effective length of database: 367
Effective search space:   111568
Effective search space used:   111568
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.

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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