GapMind for catabolism of small carbon sources

 

Aligments for a candidate for icd in Dinoroseobacter shibae DFL-12

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate 3610012 Dshi_3393 3-isopropylmalate dehydrogenase (RefSeq)

Query= BRENDA::P33197
         (496 letters)



>lcl|FitnessBrowser__Dino:3610012 Dshi_3393 3-isopropylmalate
           dehydrogenase (RefSeq)
          Length = 357

 Score =  190 bits (483), Expect = 6e-53
 Identities = 138/360 (38%), Positives = 196/360 (54%), Gaps = 34/360 (9%)

Query: 22  ITVIPGDGIGPECVEATLKVLE-----AAKAPLAYEVREAGASVFRRGIASGVPQETIES 76
           ITV  GDGIGPE +  TL +L      AA   L ++    GA  + +     +P+ ++++
Sbjct: 6   ITVFDGDGIGPEIMAPTLGLLRKLAGTAATYDLNFDSHPMGAGHYAQ-TGQALPRASLDA 64

Query: 77  IRKTRVVLKGPLETP-VGYG---EKSANVTLRKLFETYANVRPVREFPNVPTPYAGRG-I 131
            R +  +L   +  P + Y    E +  + +R   + YA VRPVR  P  PTP    G +
Sbjct: 65  ARASDAILLSAMGLPDIRYPDGTEITPQIDIRIALDLYAGVRPVRIVPGHPTPLHAPGPV 124

Query: 132 DLVVVRENVEDLY--AGIEHMQTPSVAQTLKLISWKGSEKIVRFAFELA-------RAEG 182
           D V++RE+ E L+   G   +      +TL+ I+   SEK+ RFAF LA       R EG
Sbjct: 125 DFVLIRESTEGLFHTKGKGTVTKDHATETLQ-ITRDTSEKLFRFAFALAAQRKASGRGEG 183

Query: 183 RKKVHCATKSNIMKLAEGTLKRAFEQVAQEYPDIEAVHIIVDNAAHQLVKRPEQFEVIVT 242
           R  V C  K+N+ + A    +  F+  A  +PD+ A H  VD  A  +V RP+ F+V+VT
Sbjct: 184 R--VTCVDKANVFR-AFAFFREIFDAEAARHPDLIADHAYVDAMALWMVTRPQTFDVMVT 240

Query: 243 TNMNGDILSDLTSGLIGGLGFAPSANIGNEVAIFEAVHGSAPKYAGKNVINPTAVLLSAV 302
            NM GDILSDL +GL+GGLG APSA+IG++ A+F+  HG+AP  AG+ + NP A++LSA 
Sbjct: 241 ENMFGDILSDLGAGLMGGLGLAPSADIGDDNAVFQPCHGTAPDIAGRGIANPLAMILSAA 300

Query: 303 MMLRYL------EEFAT-ADLIENALLYTLEEGRVLTGDVVGYDRGAKTTEYTEAIIQNL 355
           MML +L       E AT    +  A+   L EGRVLT D+ G    A T E   A+   L
Sbjct: 301 MMLDWLALRGQNAELATDGQRLREAVEAVLTEGRVLTRDLGG---NASTEEAAAAVAAKL 357


Lambda     K      H
   0.317    0.136    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: 414
Number of extensions: 28
Number of successful extensions: 5
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: 496
Length of database: 357
Length adjustment: 32
Effective length of query: 464
Effective length of database: 325
Effective search space:   150800
Effective search space used:   150800
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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