Alignments for a candidate for icd in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Escherichia coli BW25113

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42); [Isocitrate dehydrogenase (NADP+)] kinase (EC 2.7.11.5) (characterized)
to candidate 15258 b1136 isocitrate dehydrogenase (NCBI)

Query= BRENDA::P08200
         (416 letters)



>FitnessBrowser__Keio:15258
          Length = 416

 Score =  838 bits (2166), Expect = 0.0
 Identities = 416/416 (100%), Positives = 416/416 (100%)

Query: 1   MESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGE 60
           MESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGE
Sbjct: 1   MESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGE 60

Query: 61  RKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQ 120
           RKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQ
Sbjct: 61  RKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQ 120

Query: 121 ELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLR 180
           ELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLR
Sbjct: 121 ELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLR 180

Query: 181 EEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGA 240
           EEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGA
Sbjct: 181 EEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGA 240

Query: 241 FKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIA 300
           FKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIA
Sbjct: 241 FKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIA 300

Query: 301 CMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSA 360
           CMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSA
Sbjct: 301 CMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSA 360

Query: 361 EMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM 416
           EMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM
Sbjct: 361 EMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM 416


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: 796
Number of extensions: 15
Number of successful extensions: 1
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: 416
Length adjustment: 31
Effective length of query: 385
Effective length of database: 385
Effective search space:   148225
Effective search space used:   148225
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 15258 b1136 (isocitrate dehydrogenase (NCBI))
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.32321.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.5e-246  802.6   0.7   3.9e-246  802.4   0.7    1.0  1  lcl|FitnessBrowser__Keio:15258  b1136 isocitrate dehydrogenase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15258  b1136 isocitrate dehydrogenase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  802.4   0.7  3.9e-246  3.9e-246       1     416 [.       1     416 []       1     416 [] 1.00

  Alignments for each domain:
  == domain 1  score: 802.4 bits;  conditional E-value: 3.9e-246
                       TIGR00183   1 leekvkppeeGekitlkngklvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevyaGekayelyg 79 
                                     +e+kv++p++G+kitl+ngkl+vp+npiipyieGdGiGvd++pa+ kv+daavekaykge+ki+w+e+y+Gek++++yg
  lcl|FitnessBrowser__Keio:15258   1 MESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEIYTGEKSTQVYG 79 
                                     689**************************************************************************** PP

                       TIGR00183  80 eeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvpspvkepekvdlvifrented 158
                                     ++ +lp++tld+i+ey+vaikGplttpvGgGirslnvalrqeldly+clrpvryy+g+pspvk+pe +d+vifren+ed
  lcl|FitnessBrowser__Keio:15258  80 QDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSED 158
                                     ******************************************************************************* PP

                       TIGR00183 159 iyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtkrlvrkaieyaiendkksvtlvhkGnimkft 237
                                     iyaGiew+++s++a+k+ikfl++e++vkkir+pe++GiGikp+seegtkrlvr+aieyai+nd++svtlvhkGnimkft
  lcl|FitnessBrowser__Keio:15258 159 IYAGIEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFT 237
                                     ******************************************************************************* PP

                       TIGR00183 238 eGafkdwGyelakkefgeevitkalwdklknpeeGkkivvkdriadallqqiltrpdeydviatmnlnGdylsdalaal 316
                                     eGafkdwGy+la++efg e+i+ ++w k+knp++Gk+iv+kd+iada+lqqil+rp+eydvia+mnlnGdy+sdalaa+
  lcl|FitnessBrowser__Keio:15258 238 EGAFKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIACMNLNGDYISDALAAQ 316
                                     ******************************************************************************* PP

                       TIGR00183 317 vGGlGiapGanigdevaifeathGtapkyaGldkvnpgsvilsgvllleflGwkeaadlivkalekaiaskevtydlar 395
                                     vGG+GiapGanigde+a+feathGtapkyaG+dkvnpgs+ils++++l+++Gw+eaadlivk++e ai++k+vtyd++r
  lcl|FitnessBrowser__Keio:15258 317 VGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFER 395
                                     ******************************************************************************* PP

                       TIGR00183 396 lmdgakevkcsefaeaivenl 416
                                     lmdgak +kcsef++ai+en+
  lcl|FitnessBrowser__Keio:15258 396 LMDGAKLLKCSEFGDAIIENM 416
                                     ********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (416 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.00
//
[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