GapMind for Amino acid biosynthesis

 

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

Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate 351385 BT1857 3-isopropylmalate dehydrogenase (NCBI ptt file)

Query= BRENDA::Q58991
         (347 letters)



>lcl|FitnessBrowser__Btheta:351385 BT1857 3-isopropylmalate
           dehydrogenase (NCBI ptt file)
          Length = 353

 Score =  225 bits (573), Expect = 2e-63
 Identities = 139/354 (39%), Positives = 201/354 (56%), Gaps = 19/354 (5%)

Query: 3   KVCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEKA 57
           K+ V+ GDGIG E+  + + +++ + E             G + + K G+  PE+T E  
Sbjct: 4   KIAVLAGDGIGPEISVQGVDVMSAVCEKFGHKVSYEYAICGADAIDKVGDPFPEETYEVC 63

Query: 58  KEADIILFGAITSPK----PGEVKNYKSPIITLRKMFHLYANVRPINNFGIGQLIGKIAD 113
           K AD +LF A+  PK    P      +  ++ +RK   L+AN+RP+  F    LI K   
Sbjct: 64  KNADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKC--LIHKSPL 121

Query: 114 YEFLNAKNIDIVIIRENTEDLYVGRERLENDTAIAERVITRKGSERIIRFAFEYAIKNNR 173
              L  +N D + IRE T  +Y G +  +ND A      TR   ERI++ AFEYA+K  R
Sbjct: 122 RAEL-VENADFICIRELTGGMYFGEKYQDNDKAYDTNYYTRPEIERILKVAFEYAMKR-R 179

Query: 174 KKVSCIHKANVLRITDGLFLEVFNEIKKHYNIEADDYL-VDSTAMNLIKHPEKFDVIVTT 232
           K ++ + KANVL  +  L+ ++  E+  +Y     DY+ VD+ AM +I+ P  FDV+VT 
Sbjct: 180 KHLTVVDKANVLA-SSRLWRQIAQEMAPNYPEVTTDYMFVDNAAMKMIQEPAFFDVMVTE 238

Query: 233 NMFGDILSDEASALIGGLGLAPSANIGDDKALFEPVHGSAPDIAGKGIANPMASILSIAM 292
           N FGDIL+DE S + G +GL PSA+ G+   +FEP+HGS P   G  IANP+A ILS+AM
Sbjct: 239 NTFGDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVAM 298

Query: 293 LFDYIGEKEKGDLIREAVKYCLINKKVTPDL----GGDLKTKDVGDEILNYIRK 342
           LF+Y   KE+G LIR+AV   L     TP++    G    TK+VG  I++YI+K
Sbjct: 299 LFEYFDCKEEGALIRKAVDASLDENVRTPEIQVADGAKYGTKEVGQWIVDYIKK 352


Lambda     K      H
   0.319    0.140    0.397 

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: 342
Number of extensions: 19
Number of successful extensions: 6
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: 347
Length of database: 353
Length adjustment: 29
Effective length of query: 318
Effective length of database: 324
Effective search space:   103032
Effective search space used:   103032
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 (21.7 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, the preprint on GapMind for carbon sources, 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