GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuB in Paraburkholderia bryophila 376MFSha3.1

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; EC 1.1.1.85; Beta-IPM dehydrogenase (uncharacterized)
to candidate H281DRAFT_04085 H281DRAFT_04085 isocitrate dehydrogenase (NADP)

Query= curated2:O27441
         (329 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04085 H281DRAFT_04085
           isocitrate dehydrogenase (NADP)
          Length = 418

 Score =  158 bits (400), Expect = 2e-43
 Identities = 115/365 (31%), Positives = 174/365 (47%), Gaps = 62/365 (16%)

Query: 6   IAVIPGDGIGVE-------VMEAALHILNTLDLDLEFIHADAGDACLKRTGTA--LPEET 56
           I  I GDG GV+       V++AA+         + ++   AG+   K  G    LPEET
Sbjct: 31  IPFIEGDGTGVDITPVMIKVVDAAVEKAYAGKKKIHWMEIYAGEKSTKVYGPDVWLPEET 90

Query: 57  LEAVGEARATLFGA----AGESAADVIVRLRREFDLFANLRPVKSLPGVPCLYPD---LD 109
           L+ + E   ++ G      G     + V LR+E DL+  LRPV+   GVP    +    +
Sbjct: 91  LQVLKEYVVSIKGPLTTPVGGGIRSLNVALRQELDLYVCLRPVQYFKGVPSPVREPEKTN 150

Query: 110 FVIVRENTEDLYVGDEEYTPEGAVAKRII-------------------------TRTASR 144
            VI REN+ED+Y G E +  E   AK++I                         +R  + 
Sbjct: 151 MVIFRENSEDIYAGIE-WPAESEEAKKVIKFLKEEMGVKKIRFPDTSGIGIKPVSREGTE 209

Query: 145 RISQFAFQYAQKEGMQKVTAVHKANVLKKTDGIFRDEFYKVASEYPQME----------- 193
           R+ + A QYA     + VT VHK N++K T+G FRD  Y +A +    E           
Sbjct: 210 RLVRKAIQYAIDNDRRSVTLVHKGNIMKYTEGAFRDYGYALAQKEFNAELIDGGPWMKVK 269

Query: 194 ---------ATDYYVDATAMYLITQPQEFQTIVTTNLFGDILSDEAAGLIGGLGLAPSAN 244
                      D   DA    ++ +P E+  I T NL GD +SD  A  +GG+G+AP AN
Sbjct: 270 NPKTGGDIVVKDVIADAFLQQILLRPAEYDVIATLNLNGDYVSDALAAQVGGIGIAPGAN 329

Query: 245 IGEKNALFEPVHGSAPQIAGKNIANPTAMILTTTLMLKHLNKKQEAQKIEKALQKTLAEG 304
           + +  A+FE  HG+AP+ AGK+  NP + IL+  +ML+H+   + A  I K+++ ++ + 
Sbjct: 330 MSDSVAMFEATHGTAPKYAGKDYVNPGSEILSAEMMLRHMGWLEAADLIIKSMETSILQK 389

Query: 305 LVTPD 309
            VT D
Sbjct: 390 RVTYD 394


Lambda     K      H
   0.317    0.134    0.374 

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: 308
Number of extensions: 13
Number of successful extensions: 4
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: 329
Length of database: 418
Length adjustment: 30
Effective length of query: 299
Effective length of database: 388
Effective search space:   116012
Effective search space used:   116012
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 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