Alignments for a candidate for icd in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Dechlorosoma suillum PS

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate Dsui_3295 Dsui_3295 isocitrate dehydrogenase, NADP-dependent, monomeric type

Query= BRENDA::O53611
         (745 letters)



>FitnessBrowser__PS:Dsui_3295
          Length = 746

 Score = 1163 bits (3009), Expect = 0.0
 Identities = 567/742 (76%), Positives = 646/742 (87%)

Query: 1   MSAEQPTIIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTE 60
           MSA +  IIYTLTDEAPLLAT AFLPI+R F  PAG++I  SDISVAAR+LAEF DYL +
Sbjct: 1   MSAGKSKIIYTLTDEAPLLATCAFLPIIRTFTGPAGVEIAESDISVAARVLAEFSDYLRD 60

Query: 61  EQRVPDNLAELGRLTQLPDTNIIKLPNISASVPQLVAAIKELQDKGYAVPDYPADPKTDQ 120
           +Q+VPDNLAELGRLTQ PDTNIIKLPNISASV QLVA +KELQ KGYA+PDYP +P TD+
Sbjct: 61  DQKVPDNLAELGRLTQDPDTNIIKLPNISASVAQLVACVKELQAKGYAIPDYPENPTTDE 120

Query: 121 EKAIKERYARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGEWSMASRTHVAHMRH 180
           EKA+K RY +CLGSAVNPVLR+GNSDRRAP AVK YA+KHPHSMGEW   S+THVAHM H
Sbjct: 121 EKALKTRYGKCLGSAVNPVLREGNSDRRAPAAVKNYAKKHPHSMGEWKPWSQTHVAHMDH 180

Query: 181 GDFYAGEKSMTLDRARNVRMELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEE 240
           GDFY GEKS+TLD+AR+V+MEL+ KSGKTIVLKP+V L DG++IDSMFMSKKALCDFYE+
Sbjct: 181 GDFYHGEKSLTLDKARDVKMELVTKSGKTIVLKPKVALKDGEIIDSMFMSKKALCDFYEK 240

Query: 241 QMQDAFETGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLS 300
           +++D  + G++FSLHVKATMMKVSHPIVFGH V+I+YK+AF KH +LFD+LG+NVNNG++
Sbjct: 241 ELEDCRQAGILFSLHVKATMMKVSHPIVFGHCVKIYYKEAFEKHGKLFDELGINVNNGMA 300

Query: 301 DLYSKIESLPASQRDEIIEDLHRCHEHRPELAMVDSARGISNFHSPSDVIVDASMPAMIR 360
            LY KI++LP S+RDEII DLH C EHRP LAMVDSA+GI+NFHSP+D+IVDASMPAMIR
Sbjct: 301 TLYEKIDTLPESKRDEIIRDLHACQEHRPRLAMVDSAKGITNFHSPNDIIVDASMPAMIR 360

Query: 361 AGGKMYGADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQFDPTTMGTVPNVGLMAQQAE 420
            GGKM+GADGK  D KAV PESTF+RIYQE+INFCK +G FDP TMGTVPNVGLMAQ+AE
Sbjct: 361 GGGKMWGADGKPYDCKAVMPESTFARIYQEMINFCKWHGNFDPKTMGTVPNVGLMAQKAE 420

Query: 421 EYGSHDKTFEIPEDGVANIVDVATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRA 480
           EYGSHDKTFEI E G+ANIVD+ATGEVLL++NVE GDIWRMC VKD PIRDWVKLAVTRA
Sbjct: 421 EYGSHDKTFEIAEAGIANIVDLATGEVLLSQNVEEGDIWRMCQVKDEPIRDWVKLAVTRA 480

Query: 481 RISGMPVLFWLDPYRPHENELIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLD 540
           R SGMP +FWLDPYRPHE ELIKKV+ YLKDHDT GL+I IMSQVR+MR+T ER+ RGLD
Sbjct: 481 RNSGMPAVFWLDPYRPHEAELIKKVEKYLKDHDTSGLEIHIMSQVRAMRFTLERVARGLD 540

Query: 541 TIAATGNILRDYLTDLFPILELGTSAKMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEEN 600
           TI+ TGNILRDYLTDLFPI+ELGTSAKMLS+VPLMAGGGMYETGAGGSAPKHV+QLVEEN
Sbjct: 541 TISVTGNILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMYETGAGGSAPKHVQQLVEEN 600

Query: 601 HLRWDSLGEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDNDKSPSRKTGELDNR 660
           HLRWDSLGEFLAL    E++GIKTGN +AKLL KTLD A GKLLD +KSPSR+TGELDNR
Sbjct: 601 HLRWDSLGEFLALAVSLEELGIKTGNAKAKLLAKTLDEATGKLLDENKSPSRRTGELDNR 660

Query: 661 GSQFYLAMYWAQELAAQTDDQQLAEHFASLADVLTKNEDVIVRELTEVQGEPVDIGGYYA 720
           GSQFYLA+YWAQ LAAQ++D+ LA  F  LA  L +NE  IV EL  VQG+PVDIGGYY 
Sbjct: 661 GSQFYLALYWAQALAAQSEDKDLATKFGPLAKSLAENEQKIVDELKAVQGKPVDIGGYYL 720

Query: 721 PDSDMTTAVMRPSKTFNAALEA 742
            D    TAVMRPS T N+ L+A
Sbjct: 721 ADQAKVTAVMRPSATLNSLLQA 742


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: 1519
Number of extensions: 36
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: 745
Length of database: 746
Length adjustment: 40
Effective length of query: 705
Effective length of database: 706
Effective search space:   497730
Effective search space used:   497730
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 Dsui_3295 Dsui_3295 (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.19082.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 1345.4   0.0          0 1345.2   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_3295  Dsui_3295 isocitrate dehydrogena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3295  Dsui_3295 isocitrate dehydrogenase, NADP-dependent, monomeric type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1345.2   0.0         0         0       1     741 [.       1     742 [.       1     745 [. 1.00

  Alignments for each domain:
  == domain 1  score: 1345.2 bits;  conditional E-value: 0
                         TIGR00178   1 mstekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelakt 77 
                                       ms+ k+kiiytltdeapllat ++lpi+++f+++aG+e+  +dis+a+r+laef +yl ++qkv+d+laelG+l++ 
  lcl|FitnessBrowser__PS:Dsui_3295   1 MSAGKSKIIYTLTDEAPLLATCAFLPIIRTFTGPAGVEIAESDISVAARVLAEFSDYLRDDQKVPDNLAELGRLTQD 77 
                                       8999************************************************************************* PP

                         TIGR00178  78 peaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrraplavk 154
                                       p++niiklpnisasv ql+a++kelq+kGy++pdype+p+tdeek++k+ry k++GsavnpvlreGnsdrrap+avk
  lcl|FitnessBrowser__PS:Dsui_3295  78 PDTNIIKLPNISASVAQLVACVKELQAKGYAIPDYPENPTTDEEKALKTRYGKCLGSAVNPVLREGNSDRRAPAAVK 154
                                       ***************************************************************************** PP

                         TIGR00178 155 eyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgevidssvlsk 231
                                       +ya+khph+mGew   s++hvahmd+gdfy++eks++ld+a++vk+el++k+Gk++vlk+k+ l+dge+ids+++sk
  lcl|FitnessBrowser__PS:Dsui_3295 155 NYAKKHPHSMGEWKPWSQTHVAHMDHGDFYHGEKSLTLDKARDVKMELVTKSGKTIVLKPKVALKDGEIIDSMFMSK 231
                                       ***************************************************************************** PP

                         TIGR00178 232 kalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakies 308
                                       kal++f+e+e+ed ++ g+l+slh+katmmkvs+pivfGh v+++yk++f kh++l+++lG++v+nG+a ly ki++
  lcl|FitnessBrowser__PS:Dsui_3295 232 KALCDFYEKELEDCRQAGILFSLHVKATMMKVSHPIVFGHCVKIYYKEAFEKHGKLFDELGINVNNGMATLYEKIDT 308
                                       ***************************************************************************** PP

                         TIGR00178 309 lpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssya 385
                                       lp++k++ei+ dl+++ e+rp lamvds+kGitn+h+p d+ivdasmpamir +Gkm+g+dgk  d kav+p+s++a
  lcl|FitnessBrowser__PS:Dsui_3295 309 LPESKRDEIIRDLHACQEHRPRLAMVDSAKGITNFHSPNDIIVDASMPAMIRGGGKMWGADGKPYDCKAVMPESTFA 385
                                       ***************************************************************************** PP

                         TIGR00178 386 gvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvd.ssGevlleeeveagdiwrmc 461
                                       ++yq++i++ck +G+fdp tmGtvpnvGlmaqkaeeyGshdktfei ++G++++vd ++Gevll ++ve+gdiwrmc
  lcl|FitnessBrowser__PS:Dsui_3295 386 RIYQEMINFCKWHGNFDPKTMGTVPNVGLMAQKAEEYGSHDKTFEIAEAGIANIVDlATGEVLLSQNVEEGDIWRMC 462
                                       ********************************************************99******************* PP

                         TIGR00178 462 qvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGe 538
                                       qvkd pi+dwvklavtrar sg+pavfwldp+r+h++elikkvekylkdhdt+Gl+i+i+s+v+a+rf+ler++rG 
  lcl|FitnessBrowser__PS:Dsui_3295 463 QVKDEPIRDWVKLAVTRARNSGMPAVFWLDPYRPHEAELIKKVEKYLKDHDTSGLEIHIMSQVRAMRFTLERVARGL 539
                                       ***************************************************************************** PP

                         TIGR00178 539 dtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaas 615
                                       dtisvtGn+lrdyltdlfpi+elGtsakmls+vplmaGGG++etGaGGsapkhvqql+eenhlrwdslGeflala s
  lcl|FitnessBrowser__PS:Dsui_3295 540 DTISVTGNILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMYETGAGGSAPKHVQQLVEENHLRWDSLGEFLALAVS 616
                                       ***************************************************************************** PP

                         TIGR00178 616 lehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaea 692
                                       le++++ktgn+kak+la+tld+atgkllde+kspsr++Geldnrgs+fyla ywaq+laaq+edk+la +f ++a++
  lcl|FitnessBrowser__PS:Dsui_3295 617 LEELGIKTGNAKAKLLAKTLDEATGKLLDENKSPSRRTGELDNRGSQFYLALYWAQALAAQSEDKDLATKFGPLAKS 693
                                       ***************************************************************************** PP

                         TIGR00178 693 ltkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnailea 741
                                       l++ne+kiv el+avqG++vd+gGyy +d+ ++t+v+rpsat+n++l+a
  lcl|FitnessBrowser__PS:Dsui_3295 694 LAENEQKIVDELKAVQGKPVDIGGYYLADQAKVTAVMRPSATLNSLLQA 742
                                       **********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (746 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 12.49
//
[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