Alignments for a candidate for icd in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Pseudomonas stutzeri RCH2

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate GFF1980 Psest_2023 isocitrate dehydrogenase, NADP-dependent, monomeric type

Query= BRENDA::O53611
         (745 letters)



>FitnessBrowser__psRCH2:GFF1980
          Length = 742

 Score =  997 bits (2577), Expect = 0.0
 Identities = 491/736 (66%), Positives = 592/736 (80%), Gaps = 2/736 (0%)

Query: 8   IIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTEEQRVPDN 67
           IIYT TDEAP LATY+ LPIV AFA  A I +E  DIS+A RILA F D L  +++V D+
Sbjct: 7   IIYTFTDEAPALATYSLLPIVEAFAASAEIAVETRDISLAGRILASFADQLDADKKVDDD 66

Query: 68  LAELGRLTQLPDTNIIKLPNISASVPQLVAAIKELQDKGYAVPDYPADPKTDQEKAIKER 127
           LA+L  LT  PD NIIKLPNISASVPQL AAI ELQ  GY +P++P DP+TD EK  + R
Sbjct: 67  LAKLAELTNQPDANIIKLPNISASVPQLKAAIAELQALGYNIPNFPEDPQTDAEKDARAR 126

Query: 128 YARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGEWSMASRTHVAHMRHGDFYAGE 187
           Y++ LGSAVNPVLR+GNSDRRAP AVK YARKHPHSMG+WS AS++H  +MR GDF++ E
Sbjct: 127 YSKVLGSAVNPVLREGNSDRRAPAAVKAYARKHPHSMGKWSKASQSHADYMRGGDFFSSE 186

Query: 188 KSMTLDRARNVRMELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEEQMQDAFE 247
           +S+T+++A +VR+E + K GK + +K ++ L +G+V+D MFMS   L  F+EE +QD  E
Sbjct: 187 QSITMEKAGDVRIEFVGKDGK-VEVKKQLALQEGEVLDGMFMSCNKLRAFFEETLQDCKE 245

Query: 248 TGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLSDLYSKIE 307
           TGVM+SLHVKATMMK+SHPIVFGHAV ++YKD F K+ ELF +LGVN NNG+S +Y KI+
Sbjct: 246 TGVMWSLHVKATMMKISHPIVFGHAVSVYYKDVFDKYGELFKELGVNPNNGISSVYDKIK 305

Query: 308 SLPASQRDEIIEDLHRCHEHRPELAMVDSARGISNFHSPSDVIVDASMPAMIRAGGKMYG 367
           SLP SQ++EI+ D+H  + HRPE+AMVDS +GI+N H PSDVIVDASMPAMIR  G+M+G
Sbjct: 306 SLPVSQQEEILHDIHEVYAHRPEMAMVDSVKGITNLHIPSDVIVDASMPAMIRNSGQMWG 365

Query: 368 ADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQFDPTTMGTVPNVGLMAQQAEEYGSHDK 427
            DGK KDTKAV PEST++RIYQE+INFCKTNG FDP TMG+VPNVGLMAQ+AEEYGSHDK
Sbjct: 366 KDGKQKDTKAVMPESTYARIYQEMINFCKTNGAFDPVTMGSVPNVGLMAQKAEEYGSHDK 425

Query: 428 TFEIPEDGVANIVDVATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRARISGMPV 487
           TFE+  DG   +V +A G VL+   VE GDIWR C  KDAPIRDWVKLAVTRAR S  P 
Sbjct: 426 TFEMQADGTMRVV-LADGTVLMQHEVEKGDIWRACQTKDAPIRDWVKLAVTRARQSNTPA 484

Query: 488 LFWLDPYRPHENELIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLDTIAATGN 547
           +FWLDP R H+ +L +KV+TYLKDHD  GLDI+IM    ++R + ER++RG DTI+ TGN
Sbjct: 485 IFWLDPERAHDRQLQEKVETYLKDHDLSGLDIRIMGYNEAIRVSMERMIRGQDTISVTGN 544

Query: 548 ILRDYLTDLFPILELGTSAKMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEENHLRWDSL 607
           +LRDYLTDLFPI+ELGTSAKMLS+VPLMAGGGMYETGAGGSAPKHV+QLVEEN+LRWDSL
Sbjct: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMYETGAGGSAPKHVQQLVEENYLRWDSL 604

Query: 608 GEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDNDKSPSRKTGELDNRGSQFYLA 667
           GEFLAL    E+ GIKTGN +AK+LGKTLD A GKLLDN+KSP+RK G+LDNRGS FYLA
Sbjct: 605 GEFLALAVSLEETGIKTGNVKAKILGKTLDQATGKLLDNNKSPARKVGQLDNRGSHFYLA 664

Query: 668 MYWAQELAAQTDDQQLAEHFASLADVLTKNEDVIVRELTEVQGEPVDIGGYYAPDSDMTT 727
           +YWAQ LAAQ +D +L  HFA LA  LT+ E  IV EL  VQG+PVDIGGYY  + ++T+
Sbjct: 665 LYWAQALAAQDEDAELKAHFAPLAKQLTEQEATIVDELAAVQGKPVDIGGYYRSNPELTS 724

Query: 728 AVMRPSKTFNAALEAV 743
            VMRPS TFN+AL A+
Sbjct: 725 KVMRPSATFNSALAAL 740


Lambda     K      H
   0.317    0.134    0.388 

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: 1383
Number of extensions: 45
Number of successful extensions: 3
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: 745
Length of database: 742
Length adjustment: 40
Effective length of query: 705
Effective length of database: 702
Effective search space:   494910
Effective search space used:   494910
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: 55 (25.8 bits)

Align candidate GFF1980 Psest_2023 (isocitrate dehydrogenase, NADP-dependent, monomeric type)
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.16706.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 1317.7   2.3          0 1317.5   2.3    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1980  Psest_2023 isocitrate dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1980  Psest_2023 isocitrate dehydrogenase, NADP-dependent, monomeric type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1317.5   2.3         0         0       1     743 [.       1     741 [.       1     742 [] 0.99

  Alignments for each domain:
  == domain 1  score: 1317.5 bits;  conditional E-value: 0
                           TIGR00178   1 mstekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGela 75 
                                         mst+ +kiiyt tdeap+latysllpiv+afaasa i+vetrdislagrila+f ++l  ++kvdd+la+l el+
  lcl|FitnessBrowser__psRCH2:GFF1980   1 MSTP-SKIIYTFTDEAPALATYSLLPIVEAFAASAEIAVETRDISLAGRILASFADQLDADKKVDDDLAKLAELT 74 
                                         7887.9********************************************************************* PP

                           TIGR00178  76 ktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrrap 150
                                         + p+aniiklpnisasvpqlkaai elq+ Gy++p++pe+p+td+ekd +ary+k++GsavnpvlreGnsdrrap
  lcl|FitnessBrowser__psRCH2:GFF1980  75 NQPDANIIKLPNISASVPQLKAAIAELQALGYNIPNFPEDPQTDAEKDARARYSKVLGSAVNPVLREGNSDRRAP 149
                                         *************************************************************************** PP

                           TIGR00178 151 lavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgevid 225
                                         +avk yarkhph+mG+ws++s+sh   m+ gdf++se+s+++++a +v+ie++ kdGk+ v k++l l++gev+d
  lcl|FitnessBrowser__psRCH2:GFF1980 150 AAVKAYARKHPHSMGKWSKASQSHADYMRGGDFFSSEQSITMEKAGDVRIEFVGKDGKVEV-KKQLALQEGEVLD 223
                                         *********************************************************9987.778********** PP

                           TIGR00178 226 ssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGla 300
                                         ++++s + l++f+ee ++d ke+gv+ slh+katmmk+s+pivfGh+v+v+ykdvf k++el+++lG++ +nG++
  lcl|FitnessBrowser__psRCH2:GFF1980 224 GMFMSCNKLRAFFEETLQDCKETGVMWSLHVKATMMKISHPIVFGHAVSVYYKDVFDKYGELFKELGVNPNNGIS 298
                                         *************************************************************************** PP

                           TIGR00178 301 dlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdt 375
                                          +y ki+slp +++eei  d+++vy++rpe+amvds kGitnlh+psdvivdasmpamir+sG+m+gkdgk+kdt
  lcl|FitnessBrowser__psRCH2:GFF1980 299 SVYDKIKSLPVSQQEEILHDIHEVYAHRPEMAMVDSVKGITNLHIPSDVIVDASMPAMIRNSGQMWGKDGKQKDT 373
                                         *************************************************************************** PP

                           TIGR00178 376 kavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevllee 450
                                         kav+p+s+ya++yq++i++ck+nGafdp tmG+vpnvGlmaqkaeeyGshdktfe++adG++rvv ++G vl+++
  lcl|FitnessBrowser__psRCH2:GFF1980 374 KAVMPESTYARIYQEMINFCKTNGAFDPVTMGSVPNVGLMAQKAEEYGSHDKTFEMQADGTMRVVLADGTVLMQH 448
                                         *************************************************************************** PP

                           TIGR00178 451 eveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvk 525
                                         eve+gdiwr+cq kdapi+dwvklavtrar s+tpa+fwldperahd++l +kve+ylkdhd +Gldi+i+   +
  lcl|FitnessBrowser__psRCH2:GFF1980 449 EVEKGDIWRACQTKDAPIRDWVKLAVTRARQSNTPAIFWLDPERAHDRQLQEKVETYLKDHDLSGLDIRIMGYNE 523
                                         *************************************************************************** PP

                           TIGR00178 526 atrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenh 600
                                         a+r s+er+ rG+dtisvtGnvlrdyltdlfpi+elGtsakmls+vplmaGGG++etGaGGsapkhvqql+een+
  lcl|FitnessBrowser__psRCH2:GFF1980 524 AIRVSMERMIRGQDTISVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMYETGAGGSAPKHVQQLVEENY 598
                                         *************************************************************************** PP

                           TIGR00178 601 lrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaa 675
                                         lrwdslGeflala sle+ ++ktgn kak+l++tld+atgklld++ksp+rkvG+ldnrgs+fyla ywaq+laa
  lcl|FitnessBrowser__psRCH2:GFF1980 599 LRWDSLGEFLALAVSLEETGIKTGNVKAKILGKTLDQATGKLLDNNKSPARKVGQLDNRGSHFYLALYWAQALAA 673
                                         *************************************************************************** PP

                           TIGR00178 676 qtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnailealk 743
                                         q ed+el+a+fa++a+ lt++e++iv elaavqG++vd+gGyy ++ +lt+kv+rpsatfn++l+al+
  lcl|FitnessBrowser__psRCH2:GFF1980 674 QDEDAELKAHFAPLAKQLTEQEATIVDELAAVQGKPVDIGGYYRSNPELTSKVMRPSATFNSALAALN 741
                                         *****************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (742 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: 8.09
//
[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