Alignments for a candidate for icd in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Echinicola vietnamensis KMM 6221, DSM 17526

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate Echvi_1839 Echvi_1839 isocitrate dehydrogenase, NADP-dependent, monomeric type

Query= SwissProt::P16100
         (741 letters)



>FitnessBrowser__Cola:Echvi_1839
          Length = 762

 Score = 1053 bits (2724), Expect = 0.0
 Identities = 520/735 (70%), Positives = 606/735 (82%)

Query: 3   TPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKI 62
           TPKI+YTLTDEAPALATYSLLPIIK+FT S+G+ VETRDISL+GR+IA FPEYL + Q+I
Sbjct: 21  TPKILYTLTDEAPALATYSLLPIIKSFTDSAGVVVETRDISLSGRIIANFPEYLKEDQRI 80

Query: 63  SDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDV 122
            D LAELG++A TP+ANI+KLPNISAS+PQLKAAIKELQ++GY LPDYP+EPK   EK V
Sbjct: 81  GDALAELGEIAKTPEANIVKLPNISASIPQLKAAIKELQEKGYALPDYPDEPKDQEEKGV 140

Query: 123 KARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFY 182
           KA+YDKIKGSAVNPVLREGNSDRRAP +VK +AR +PH MG WSADSKSHVA M  GDFY
Sbjct: 141 KAKYDKIKGSAVNPVLREGNSDRRAPQAVKQFARNNPHSMGEWSADSKSHVASMSEGDFY 200

Query: 183 GSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIED 242
           GSE++  +   G+VKI+L A DG+ TVLK    +Q GE+IDSSVMS   L+ F+A +  D
Sbjct: 201 GSEQSLTMSEAGTVKIQLEAGDGTVTVLKEGLELQEGEVIDSSVMSVKKLQAFLAEQKAD 260

Query: 243 AKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYA 302
           AK +G+L S+H+KATMMKVSDPI+FG  V  F+     KHA  +K++G DVNNG GDL +
Sbjct: 261 AKAKGILFSLHMKATMMKVSDPIIFGHAVKVFFAPVFEKHAATIKKLGVDVNNGFGDLVS 320

Query: 303 RIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGK 362
            ++ LP  K+KEIEADI+A  A  P LAMVNS KGITNLHVPSDVI+DASMPAMIR SG+
Sbjct: 321 ALEKLPADKRKEIEADIEACLADSPDLAMVNSHKGITNLHVPSDVIIDASMPAMIRSSGQ 380

Query: 363 MWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGS 422
           MW  +  L DTKA+IPDR YAGVYQ  I+ CKQHGAFDPTTMGSVPNVGLMAQKAEEYGS
Sbjct: 381 MWNKNDALQDTKAIIPDRSYAGVYQETIDFCKQHGAFDPTTMGSVPNVGLMAQKAEEYGS 440

Query: 423 HDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNT 482
           HDKTF+  ADG ++V + +G+ L+E  VE GDI+RMCQ KDAPIQDWVKLAVNRAR++NT
Sbjct: 441 HDKTFEAAADGAIKVLNAAGETLMEHKVEKGDIFRMCQTKDAPIQDWVKLAVNRARSSNT 500

Query: 483 PAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVT 542
           PAVFWLD  RAHDAQ+I KV +YL  +DT GLDIRILSPVEATRFSL RI++GKDTISVT
Sbjct: 501 PAVFWLDEHRAHDAQLIQKVNQYLPQHDTEGLDIRILSPVEATRFSLERIKDGKDTISVT 560

Query: 543 GNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWD 602
           GNVLRDYLTDLFPI+ELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQF+EEG+LRWD
Sbjct: 561 GNVLRDYLTDLFPILELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQFVEEGHLRWD 620

Query: 603 SLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFY 662
           SLGEFLALA SLEHLG  + N +A+VL  TLD ATGK L+N KSP+RKV E+DNRGSHFY
Sbjct: 621 SLGEFLALAVSLEHLGETFDNNRAIVLGKTLDTATGKFLENGKSPSRKVNELDNRGSHFY 680

Query: 663 LALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDL 722
           LA+YWA+ALA Q ED  L+  FT +AKA+ + E +++ EL  AQG PVDI GY+ P  D 
Sbjct: 681 LAMYWAEALANQDEDAALKEIFTKVAKAMIEKEEQVIAELNGAQGSPVDIGGYFKPAEDK 740

Query: 723 TSKAIRPSATFNAAL 737
           TSKA+RPS T N  L
Sbjct: 741 TSKAMRPSQTLNGIL 755


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: 1506
Number of extensions: 50
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: 762
Length adjustment: 40
Effective length of query: 701
Effective length of database: 722
Effective search space:   506122
Effective search space used:   506122
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 Echvi_1839 Echvi_1839 (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.32491.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 1325.0   2.3          0 1324.8   2.3    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1839  Echvi_1839 isocitrate dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1839  Echvi_1839 isocitrate dehydrogenase, NADP-dependent, monomeric type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1324.8   2.3         0         0       3     742 ..      19     758 ..      16     760 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1324.8 bits;  conditional E-value: 0
                            TIGR00178   3 tekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelak 76 
                                          t+++ki+ytltdeap+latysllpi+k+f++saG+ vetrdisl+gri+a+fpeyl e+q+++dalaelGe+ak
  lcl|FitnessBrowser__Cola:Echvi_1839  19 TKTPKILYTLTDEAPALATYSLLPIIKSFTDSAGVVVETRDISLSGRIIANFPEYLKEDQRIGDALAELGEIAK 92 
                                          6789********************************************************************** PP

                            TIGR00178  77 tpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrrap 150
                                          tpeani+klpnisas+pqlkaaikelq+kGy+lpdyp+epk +eek +ka+y+kikGsavnpvlreGnsdrrap
  lcl|FitnessBrowser__Cola:Echvi_1839  93 TPEANIVKLPNISASIPQLKAAIKELQEKGYALPDYPDEPKDQEEKGVKAKYDKIKGSAVNPVLREGNSDRRAP 166
                                          ************************************************************************** PP

                            TIGR00178 151 lavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgevi 224
                                          +avk++ar++ph+mGewsadskshva m++gdfy+se+s+++ +a  vki+l a dG++tvlk+ l+l++gevi
  lcl|FitnessBrowser__Cola:Echvi_1839 167 QAVKQFARNNPHSMGEWSADSKSHVASMSEGDFYGSEQSLTMSEAGTVKIQLEAGDGTVTVLKEGLELQEGEVI 240
                                          ************************************************************************** PP

                            TIGR00178 225 dssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenG 298
                                          dssv+s k l++fl+e+ +dak++g+l+slh+katmmkvsdpi+fGh+v+vf++ vf kha+++++lG+dv+nG
  lcl|FitnessBrowser__Cola:Echvi_1839 241 DSSVMSVKKLQAFLAEQKADAKAKGILFSLHMKATMMKVSDPIIFGHAVKVFFAPVFEKHAATIKKLGVDVNNG 314
                                          ************************************************************************** PP

                            TIGR00178 299 ladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgkl 372
                                          ++dl + +e+lpa k++eiead+e+++++ p+lamv+s kGitnlhvpsdvi+dasmpamir+sG+m++k++ l
  lcl|FitnessBrowser__Cola:Echvi_1839 315 FGDLVSALEKLPADKRKEIEADIEACLADSPDLAMVNSHKGITNLHVPSDVIIDASMPAMIRSSGQMWNKNDAL 388
                                          ************************************************************************** PP

                            TIGR00178 373 kdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGev 446
                                          +dtka+ipd+syagvyq+ i++ck++GafdpttmG+vpnvGlmaqkaeeyGshdktfe  adG ++v ++ Ge 
  lcl|FitnessBrowser__Cola:Echvi_1839 389 QDTKAIIPDRSYAGVYQETIDFCKQHGAFDPTTMGSVPNVGLMAQKAEEYGSHDKTFEAAADGAIKVLNAAGET 462
                                          ************************************************************************** PP

                            TIGR00178 447 lleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqi 520
                                          l+e++ve+gdi+rmcq kdapiqdwvklav+rar s+tpavfwld++rahd++li+kv++yl +hdteGldi+i
  lcl|FitnessBrowser__Cola:Echvi_1839 463 LMEHKVEKGDIFRMCQTKDAPIQDWVKLAVNRARSSNTPAVFWLDEHRAHDAQLIQKVNQYLPQHDTEGLDIRI 536
                                          ************************************************************************** PP

                            TIGR00178 521 lspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqq 594
                                          lspv+atrfsleri+ G+dtisvtGnvlrdyltdlfpilelGtsakmls+vplm+GGGlfetGaGGsapkhvqq
  lcl|FitnessBrowser__Cola:Echvi_1839 537 LSPVEATRFSLERIKDGKDTISVTGNVLRDYLTDLFPILELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQ 610
                                          ************************************************************************** PP

                            TIGR00178 595 leeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylaky 668
                                          ++ee+hlrwdslGeflala sleh++ + +n++a vl++tld atgk+l++ kspsrkv eldnrgs+fyla+y
  lcl|FitnessBrowser__Cola:Echvi_1839 611 FVEEGHLRWDSLGEFLALAVSLEHLGETFDNNRAIVLGKTLDTATGKFLENGKSPSRKVNELDNRGSHFYLAMY 684
                                          ************************************************************************** PP

                            TIGR00178 669 waqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnaileal 742
                                          wa++la q ed+ l++ f+ va+a+ ++ee+++ael+ +qG++vd+gGy++p +d+t+k++rps+t+n ile +
  lcl|FitnessBrowser__Cola:Echvi_1839 685 WAEALANQDEDAALKEIFTKVAKAMIEKEEQVIAELNGAQGSPVDIGGYFKPAEDKTSKAMRPSQTLNGILEMV 758
                                          ***********************************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (762 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 10.47
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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, or view the source code.

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