Alignments for a candidate for icd in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Dechlorosoma suillum PS

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42); [Isocitrate dehydrogenase (NADP+)] kinase (EC 2.7.11.5) (characterized)
to candidate Dsui_3296 Dsui_3296 isocitrate dehydrogenase, NADP-dependent, prokaryotic type

Query= BRENDA::P08200
         (416 letters)



>FitnessBrowser__PS:Dsui_3296
          Length = 408

 Score =  599 bits (1544), Expect = e-176
 Identities = 301/416 (72%), Positives = 341/416 (81%), Gaps = 8/416 (1%)

Query: 1   MESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGE 60
           M S + VP  G+KI         P +PIIP+IEGDGIGVD+TP M+KVVDAAV+KAY G+
Sbjct: 1   MSSHIKVPQGGQKIIPGQP---TPNHPIIPFIEGDGIGVDITPVMIKVVDAAVQKAYGGQ 57

Query: 61  RKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQ 120
           +KI WME+Y GEKST++YG D WLP ET D ++EY V+IKGP+TTPVGGGIRSLNVALRQ
Sbjct: 58  KKIHWMEVYAGEKSTRIYGADEWLPKETFDALKEYSVSIKGPMTTPVGGGIRSLNVALRQ 117

Query: 121 ELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLR 180
           ELDLY C+RPV+Y++G PSP+K PEL +MVIFREN+EDIYAGIEW   S   +KVIKFL+
Sbjct: 118 ELDLYQCVRPVQYFKGVPSPLKQPELCNMVIFRENTEDIYAGIEWAHGSEACKKVIKFLQ 177

Query: 181 EEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGA 240
           EEMGVKKIRFPE  GIGIKP S EGT+RLVRAAI+YAI N R SVT+VHKGNIMKFTEG 
Sbjct: 178 EEMGVKKIRFPESSGIGIKPISVEGTERLVRAAIKYAIDNGRKSVTIVHKGNIMKFTEGN 237

Query: 241 FKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIA 300
           F+D  Y LA+ EFGG  IDGGPW K+ N      IVIKD IADAFLQQILLRPAEYDVIA
Sbjct: 238 FRDTAYALAKREFGGVDIDGGPWQKLPN-----GIVIKDAIADAFLQQILLRPAEYDVIA 292

Query: 301 CMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSA 360
             NLNGDYISDALAAQVGGIGIAPGANI D+ A FEATHGTAPKYAG+DKVNPGS+ILSA
Sbjct: 293 TTNLNGDYISDALAAQVGGIGIAPGANISDQYACFEATHGTAPKYAGKDKVNPGSLILSA 352

Query: 361 EMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM 416
           EMMLRH+GW EAADLI+K ME AI  K VTYDF RLM+GA  + CSEFG+A+I  M
Sbjct: 353 EMMLRHLGWKEAADLIIKSMEAAIGDKVVTYDFARLMEGATEVSCSEFGEAMIARM 408


Lambda     K      H
   0.318    0.138    0.408 

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: 646
Number of extensions: 19
Number of successful extensions: 2
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: 416
Length of database: 408
Length adjustment: 31
Effective length of query: 385
Effective length of database: 377
Effective search space:   145145
Effective search space used:   145145
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)

Align candidate Dsui_3296 Dsui_3296 (isocitrate dehydrogenase, NADP-dependent, prokaryotic type)
to HMM TIGR00183 (icd: isocitrate dehydrogenase, NADP-dependent (EC 1.1.1.42))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00183.hmm
# target sequence database:        /tmp/gapView.11259.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00183  [M=417]
Accession:   TIGR00183
Description: prok_nadp_idh: isocitrate dehydrogenase, NADP-dependent
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     2e-213  694.7   0.6   2.2e-213  694.5   0.6    1.0  1  lcl|FitnessBrowser__PS:Dsui_3296  Dsui_3296 isocitrate dehydrogena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3296  Dsui_3296 isocitrate dehydrogenase, NADP-dependent, prokaryotic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  694.5   0.6  2.2e-213  2.2e-213       3     416 ..       3     408 .]       1     408 [] 0.98

  Alignments for each domain:
  == domain 1  score: 694.5 bits;  conditional E-value: 2.2e-213
                         TIGR00183   3 ekvkppeeGekitlkngklvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevyaGekayelyg 79 
                                       +++k+p+ G+ki    g+   pn+piip+ieGdGiGvdi+p +ikv+daav+kay+g+kki w+evyaGek++++yg
  lcl|FitnessBrowser__PS:Dsui_3296   3 SHIKVPQGGQKIIP--GQ-PTPNHPIIPFIEGDGIGVDITPVMIKVVDAAVQKAYGGQKKIHWMEVYAGEKSTRIYG 76 
                                       67888888888864..33.46******************************************************** PP

                         TIGR00183  80 eeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvpspvkepekvdlvifrent 156
                                        +e+lp++t+da+key+v+ikGp+ttpvGgGirslnvalrqeldly c+rpv+y+kgvpsp+k+pe  ++vifrent
  lcl|FitnessBrowser__PS:Dsui_3296  77 ADEWLPKETFDALKEYSVSIKGPMTTPVGGGIRSLNVALRQELDLYQCVRPVQYFKGVPSPLKQPELCNMVIFRENT 153
                                       ***************************************************************************** PP

                         TIGR00183 157 ediyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtkrlvrkaieyaiendkksvtlvhkGni 233
                                       ediyaGiewa+gse +kk+ikfl++e++vkkir+pe+sGiGikpis egt+rlvr+ai+yai+n +ksvt+vhkGni
  lcl|FitnessBrowser__PS:Dsui_3296 154 EDIYAGIEWAHGSEACKKVIKFLQEEMGVKKIRFPESSGIGIKPISVEGTERLVRAAIKYAIDNGRKSVTIVHKGNI 230
                                       ***************************************************************************** PP

                         TIGR00183 234 mkfteGafkdwGyelakkefgeevitkalwdklknpeeGkkivvkdriadallqqiltrpdeydviatmnlnGdyls 310
                                       mkfteG f+d  y+lak+efg   i+ ++w+kl n      iv+kd iada+lqqil+rp+eydviat nlnGdy+s
  lcl|FitnessBrowser__PS:Dsui_3296 231 MKFTEGNFRDTAYALAKREFGGVDIDGGPWQKLPN-----GIVIKDAIADAFLQQILLRPAEYDVIATTNLNGDYIS 302
                                       *********************************99.....58*********************************** PP

                         TIGR00183 311 dalaalvGGlGiapGanigdevaifeathGtapkyaGldkvnpgsvilsgvllleflGwkeaadlivkalekaiask 387
                                       dalaa+vGG+GiapGani+d+ a feathGtapkyaG+dkvnpgs+ils++++l++lGwkeaadli+k++e+ai +k
  lcl|FitnessBrowser__PS:Dsui_3296 303 DALAAQVGGIGIAPGANISDQYACFEATHGTAPKYAGKDKVNPGSLILSAEMMLRHLGWKEAADLIIKSMEAAIGDK 379
                                       ***************************************************************************** PP

                         TIGR00183 388 evtydlarlmdgakevkcsefaeaivenl 416
                                       +vtyd+arlm+ga+ev csef+ea++ ++
  lcl|FitnessBrowser__PS:Dsui_3296 380 VVTYDFARLMEGATEVSCSEFGEAMIARM 408
                                       **************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (408 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.41
//
[ok]

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources