Alignments for a candidate for icd in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Pseudomonas putida KT2440

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate PP_4012 PP_4012 isocitrate dehydrogenase

Query= SwissProt::P16100
         (741 letters)



>FitnessBrowser__Putida:PP_4012
          Length = 741

 Score = 1156 bits (2991), Expect = 0.0
 Identities = 577/736 (78%), Positives = 643/736 (87%)

Query: 5   KIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKISD 64
           KIIYT TDEAPALATYSLLPII+AFT S+ IAVETRDISLAGR++A FPE L   +++ D
Sbjct: 6   KIIYTFTDEAPALATYSLLPIIEAFTASADIAVETRDISLAGRILAAFPEQLGAEKQVGD 65

Query: 65  DLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDVKA 124
            LAELG+LATTP+ANIIKLPNISASVPQLKAAIKELQ +G+ +PDY +EP T  EK+ +A
Sbjct: 66  HLAELGQLATTPEANIIKLPNISASVPQLKAAIKELQGKGFNIPDYADEPATAEEKESRA 125

Query: 125 RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFYGS 184
           RYD+IKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAW+ADSKSHVAHM  GDFYGS
Sbjct: 126 RYDRIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWAADSKSHVAHMTQGDFYGS 185

Query: 185 EKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAK 244
           EKAALI A  S++IEL+ KDGS+TVLK KT+V+A E+ID + MS+ AL+ FIA +I DAK
Sbjct: 186 EKAALIEADDSLRIELVGKDGSTTVLKEKTAVKAAEVIDCATMSRKALKAFIAEQIADAK 245

Query: 245 KQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARI 304
             GVLLSVHLKATMMKVSDPIMFG IV EFY D LTKHA  L ++GF+ NNGIGDLYARI
Sbjct: 246 AAGVLLSVHLKATMMKVSDPIMFGVIVEEFYNDVLTKHAAALAEVGFNANNGIGDLYARI 305

Query: 305 KTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364
           K LP  KQ EIEADIQA+YA+RP LAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW
Sbjct: 306 KDLPADKQAEIEADIQALYAERPALAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 365

Query: 365 GPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGSHD 424
              G+L D KAVIPDRCYAG+YQ  IEDCK +GAFDPTTMGSVPNVGLMAQKAEEYGSHD
Sbjct: 366 NAAGELQDAKAVIPDRCYAGIYQATIEDCKVNGAFDPTTMGSVPNVGLMAQKAEEYGSHD 425

Query: 425 KTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNTPA 484
           KTFQI ADGVVRV D  G ++LEQ+VEAGDI+RMCQ KDAPIQDWVKLAVNRAR +NTPA
Sbjct: 426 KTFQIKADGVVRVVDGKGNVVLEQNVEAGDIFRMCQTKDAPIQDWVKLAVNRARLSNTPA 485

Query: 485 VFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVTGN 544
           VFWLDPARAHD  +I KV++YLKD+DT+GLDIRIL+PV+A +FSLARIREGKDTISVTGN
Sbjct: 486 VFWLDPARAHDGVMIEKVQKYLKDHDTTGLDIRILAPVDAIKFSLARIREGKDTISVTGN 545

Query: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWDSL 604
           VLRDYLTDLFPIMELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQ +EE +LRWDSL
Sbjct: 546 VLRDYLTDLFPIMELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQLVEENFLRWDSL 605

Query: 605 GEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFYLA 664
           GEFLALAASLEHLGN Y NP+A VLA+TLDQATGK LD NKSP+RKVG IDNRGSHFYL 
Sbjct: 606 GEFLALAASLEHLGNTYDNPRAKVLANTLDQATGKFLDTNKSPSRKVGGIDNRGSHFYLT 665

Query: 665 LYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDLTS 724
           LYWA+ALAAQT+D  LQA+F  +AK L +NE  IV EL A QGKP DI GYY P+ +LT+
Sbjct: 666 LYWAEALAAQTDDAALQARFAPLAKTLAENEATIVAELNAVQGKPADIGGYYAPDAELTA 725

Query: 725 KAIRPSATFNAALAPL 740
           K +RPS T N+A+A L
Sbjct: 726 KVMRPSQTLNSAIAAL 741


Lambda     K      H
   0.315    0.131    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: 1537
Number of extensions: 48
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: 741
Length of database: 741
Length adjustment: 40
Effective length of query: 701
Effective length of database: 701
Effective search space:   491401
Effective search space used:   491401
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 (21.5 bits)
S2: 55 (25.8 bits)

Align candidate PP_4012 PP_4012 (isocitrate dehydrogenase)
to HMM TIGR00178 (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/TIGR00178.hmm
# target sequence database:        /tmp/gapView.11905.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00178  [M=744]
Accession:   TIGR00178
Description: monomer_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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
          0 1363.3   5.1          0 1363.1   5.1    1.0  1  lcl|FitnessBrowser__Putida:PP_4012  PP_4012 isocitrate dehydrogenase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4012  PP_4012 isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1363.1   5.1         0         0       5     742 ..       4     741 .]       1     741 [] 1.00

  Alignments for each domain:
  == domain 1  score: 1363.1 bits;  conditional E-value: 0
                           TIGR00178   5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelaktpe 79 
                                         ++kiiyt tdeap+latysllpi++af+asa i+vetrdislagrila fpe+l  e++v+d+laelG+la+tpe
  lcl|FitnessBrowser__Putida:PP_4012   4 RSKIIYTFTDEAPALATYSLLPIIEAFTASADIAVETRDISLAGRILAAFPEQLGAEKQVGDHLAELGQLATTPE 78 
                                         59************************************************************************* PP

                           TIGR00178  80 aniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrraplavk 154
                                         aniiklpnisasvpqlkaaikelq kG+++pdy +ep t eek+ +ary++ikGsavnpvlreGnsdrrapl+vk
  lcl|FitnessBrowser__Putida:PP_4012  79 ANIIKLPNISASVPQLKAAIKELQGKGFNIPDYADEPATAEEKESRARYDRIKGSAVNPVLREGNSDRRAPLSVK 153
                                         *************************************************************************** PP

                           TIGR00178 155 eyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgevidssvl 229
                                         +yarkhphkmG+w+adskshvahm++gdfy+sek++l++a ++++iel+ kdG++tvlk+k+ +++ evid++ +
  lcl|FitnessBrowser__Putida:PP_4012 154 NYARKHPHKMGAWAADSKSHVAHMTQGDFYGSEKAALIEADDSLRIELVGKDGSTTVLKEKTAVKAAEVIDCATM 228
                                         *************************************************************************** PP

                           TIGR00178 230 skkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlya 304
                                         s+kal++f++e+i+dak+ gvlls+hlkatmmkvsdpi+fG +v +fy+dv++kha+ l ++G++++nG++dlya
  lcl|FitnessBrowser__Putida:PP_4012 229 SRKALKAFIAEQIADAKAAGVLLSVHLKATMMKVSDPIMFGVIVEEFYNDVLTKHAAALAEVGFNANNGIGDLYA 303
                                         *************************************************************************** PP

                           TIGR00178 305 kieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavi 379
                                         +i+ lpa k+ eiead+++ y+erp lamv+sdkGitnlhvpsdvivdasmpamir+sGkm+++ g+l+d+kavi
  lcl|FitnessBrowser__Putida:PP_4012 304 RIKDLPADKQAEIEADIQALYAERPALAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMWNAAGELQDAKAVI 378
                                         *************************************************************************** PP

                           TIGR00178 380 pdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeevea 454
                                         pd++yag+yqa iedck nGafdpttmG+vpnvGlmaqkaeeyGshdktf+i+adGvvrvvd +G+v+le++vea
  lcl|FitnessBrowser__Putida:PP_4012 379 PDRCYAGIYQATIEDCKVNGAFDPTTMGSVPNVGLMAQKAEEYGSHDKTFQIKADGVVRVVDGKGNVVLEQNVEA 453
                                         *************************************************************************** PP

                           TIGR00178 455 gdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrf 529
                                         gdi+rmcq kdapiqdwvklav+rarls+tpavfwldp+rahd  +i+kv+kylkdhdt+Gldi+il pv+a++f
  lcl|FitnessBrowser__Putida:PP_4012 454 GDIFRMCQTKDAPIQDWVKLAVNRARLSNTPAVFWLDPARAHDGVMIEKVQKYLKDHDTTGLDIRILAPVDAIKF 528
                                         *************************************************************************** PP

                           TIGR00178 530 slerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwd 604
                                         sl+rir+G+dtisvtGnvlrdyltdlfpi+elGtsakmls+vplm+GGGlfetGaGGsapkhvqql+een+lrwd
  lcl|FitnessBrowser__Putida:PP_4012 529 SLARIREGKDTISVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQLVEENFLRWD 603
                                         *************************************************************************** PP

                           TIGR00178 605 slGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqted 679
                                         slGeflalaasleh++++++n++akvla+tld+atgk+ld++kspsrkvG +dnrgs+fyl+ ywa++laaqt+d
  lcl|FitnessBrowser__Putida:PP_4012 604 SLGEFLALAASLEHLGNTYDNPRAKVLANTLDQATGKFLDTNKSPSRKVGGIDNRGSHFYLTLYWAEALAAQTDD 678
                                         *************************************************************************** PP

                           TIGR00178 680 kelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnaileal 742
                                         + l+a+fa++a++l++ne++ivael+avqG++ d+gGyyapd +lt kv+rps+t+n++++al
  lcl|FitnessBrowser__Putida:PP_4012 679 AALQARFAPLAKTLAENEATIVAELNAVQGKPADIGGYYAPDAELTAKVMRPSQTLNSAIAAL 741
                                         ***********************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (741 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 7.99
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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