Alignments for a candidate for icd in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Klebsiella michiganensis M5al

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42); [Isocitrate dehydrogenase (NADP+)] kinase (EC 2.7.11.5) (characterized)
to candidate BWI76_RS11330 BWI76_RS11330 isocitrate dehydrogenase (NADP(+))

Query= BRENDA::P08200
         (416 letters)



>FitnessBrowser__Koxy:BWI76_RS11330
          Length = 416

 Score =  809 bits (2090), Expect = 0.0
 Identities = 397/416 (95%), Positives = 409/416 (98%)

Query: 1   MESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGE 60
           MESKVVVPA+G+KITLQNGKLNVP NPIIP+IEGDGIGVDVTPAMLKVVDAAVEKAYKGE
Sbjct: 1   MESKVVVPAEGQKITLQNGKLNVPNNPIIPFIEGDGIGVDVTPAMLKVVDAAVEKAYKGE 60

Query: 61  RKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQ 120
           RKISWME+YTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQ
Sbjct: 61  RKISWMEVYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQ 120

Query: 121 ELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLR 180
           ELDLY+CLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSA+A+KVIKFLR
Sbjct: 121 ELDLYVCLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSAEADKVIKFLR 180

Query: 181 EEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGA 240
           +EMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAI NDRDS+TLVHKGNIMKFTEGA
Sbjct: 181 DEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAITNDRDSLTLVHKGNIMKFTEGA 240

Query: 241 FKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIA 300
           FKDWGYQLAREEFGGELIDGGPWLK+KNPNTGKEIV+KDVIADAFLQQILLRPAEYDVIA
Sbjct: 241 FKDWGYQLAREEFGGELIDGGPWLKIKNPNTGKEIVVKDVIADAFLQQILLRPAEYDVIA 300

Query: 301 CMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSA 360
           CMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSA
Sbjct: 301 CMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSA 360

Query: 361 EMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM 416
           EMMLRHM W EAADLIVKG EGAI AKTVTYDFERLM+GAKLLKCSEFGDAII NM
Sbjct: 361 EMMLRHMQWFEAADLIVKGTEGAIAAKTVTYDFERLMEGAKLLKCSEFGDAIIANM 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: 772
Number of extensions: 16
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 BWI76_RS11330 BWI76_RS11330 (isocitrate dehydrogenase (NADP(+)))
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.13758.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.5e-242  789.9   0.3   2.7e-242  789.8   0.3    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS11330  BWI76_RS11330 isocitrate dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS11330  BWI76_RS11330 isocitrate dehydrogenase (NADP(+))
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  789.8   0.3  2.7e-242  2.7e-242       1     416 [.       1     416 []       1     416 [] 1.00

  Alignments for each domain:
  == domain 1  score: 789.8 bits;  conditional E-value: 2.7e-242
                               TIGR00183   1 leekvkppeeGekitlkngklvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevyaG 71 
                                             +e+kv++p+eG+kitl+ngkl+vpnnpiip+ieGdGiGvd++pa+ kv+daavekaykge+ki+w+evy+G
  lcl|FitnessBrowser__Koxy:BWI76_RS11330   1 MESKVVVPAEGQKITLQNGKLNVPNNPIIPFIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEVYTG 71 
                                             689******************************************************************** PP

                               TIGR00183  72 ekayelygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvpspvk 142
                                             ek++++yg++ +lp++tld+i+ey+vaikGplttpvGgGirslnvalrqeldlyvclrpvryy+g+pspvk
  lcl|FitnessBrowser__Koxy:BWI76_RS11330  72 EKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQELDLYVCLRPVRYYQGTPSPVK 142
                                             *********************************************************************** PP

                               TIGR00183 143 epekvdlvifrentediyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtkrlvrka 213
                                             +pe +d+vifren+ediyaGiew+++s+ea k+ikfl++e++vkkir+pe++GiGikp+seegtkrlvr+a
  lcl|FitnessBrowser__Koxy:BWI76_RS11330 143 HPELTDMVIFRENSEDIYAGIEWKADSAEADKVIKFLRDEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAA 213
                                             *********************************************************************** PP

                               TIGR00183 214 ieyaiendkksvtlvhkGnimkfteGafkdwGyelakkefgeevitkalwdklknpeeGkkivvkdriada 284
                                             ieyai+nd++s+tlvhkGnimkfteGafkdwGy+la++efg e+i+ ++w k+knp++Gk+ivvkd+iada
  lcl|FitnessBrowser__Koxy:BWI76_RS11330 214 IEYAITNDRDSLTLVHKGNIMKFTEGAFKDWGYQLAREEFGGELIDGGPWLKIKNPNTGKEIVVKDVIADA 284
                                             *********************************************************************** PP

                               TIGR00183 285 llqqiltrpdeydviatmnlnGdylsdalaalvGGlGiapGanigdevaifeathGtapkyaGldkvnpgs 355
                                             +lqqil+rp+eydvia+mnlnGdy+sdalaa+vGG+GiapGanigde+a+feathGtapkyaG+dkvnpgs
  lcl|FitnessBrowser__Koxy:BWI76_RS11330 285 FLQQILLRPAEYDVIACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGS 355
                                             *********************************************************************** PP

                               TIGR00183 356 vilsgvllleflGwkeaadlivkalekaiaskevtydlarlmdgakevkcsefaeaivenl 416
                                             +ils++++l+++ w eaadlivk+ e aia+k+vtyd++rlm+gak +kcsef++ai+ n+
  lcl|FitnessBrowser__Koxy:BWI76_RS11330 356 IILSAEMMLRHMQWFEAADLIVKGTEGAIAAKTVTYDFERLMEGAKLLKCSEFGDAIIANM 416
                                             **********************************************************998 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.25
//
[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