GapMind for catabolism of small carbon sources

 

Aligments for a candidate for icd in Burkholderia phytofirmans PsJN

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate BPHYT_RS20300 BPHYT_RS20300 isocitrate dehydrogenase

Query= SwissProt::P16100
         (741 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS20300 BPHYT_RS20300 isocitrate
           dehydrogenase
          Length = 742

 Score = 1211 bits (3134), Expect = 0.0
 Identities = 608/742 (81%), Positives = 662/742 (89%), Gaps = 1/742 (0%)

Query: 1   MSTP-KIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDT 59
           MSTP KIIYTLTDEAPALATYSLLPI+KAFT SS + VETRDISLAGR+IA FP+YL+  
Sbjct: 1   MSTPPKIIYTLTDEAPALATYSLLPIVKAFTRSSDVIVETRDISLAGRIIAAFPDYLSAE 60

Query: 60  QKISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTE 119
           QK  DDLAELG L+T P+AN+IKLPNISASVPQLKAAI EL+ QGYKLP YP+   TD E
Sbjct: 61  QKGPDDLAELGGLSTRPEANVIKLPNISASVPQLKAAITELRDQGYKLPAYPDVANTDAE 120

Query: 120 KDVKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNG 179
           KDVKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHM  G
Sbjct: 121 KDVKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMSGG 180

Query: 180 DFYGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAE 239
           DFYGSEK+ALIGA GSVKIEL A DGS TVLK KT+VQAGEIID+SV+SKNALR+FI AE
Sbjct: 181 DFYGSEKSALIGAAGSVKIELTATDGSKTVLKEKTAVQAGEIIDASVLSKNALRSFIEAE 240

Query: 240 IEDAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGD 299
           I DAK +GVL SVHLKATMMKVSDPI+FG +VS FYKD LTKHA+ L Q GF+ NNGIGD
Sbjct: 241 IADAKAKGVLFSVHLKATMMKVSDPIIFGHVVSVFYKDVLTKHADALAQAGFNPNNGIGD 300

Query: 300 LYARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRD 359
           LYAR+K LP      IEADI+A Y QRPQLAMVNSDKGIT+LHVPSDVIVDASMPAMIR+
Sbjct: 301 LYARLKDLPAETVAAIEADIKAQYEQRPQLAMVNSDKGITSLHVPSDVIVDASMPAMIRE 360

Query: 360 SGKMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEE 419
           SGKMWG DG LHD KAVIPDRCYAGVYQ VIEDCK+HGAFDP TMG+VPNVGLMAQ AEE
Sbjct: 361 SGKMWGADGALHDAKAVIPDRCYAGVYQAVIEDCKKHGAFDPVTMGTVPNVGLMAQAAEE 420

Query: 420 YGSHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARA 479
           YGSHDKTFQIPA+GVVRVTD +G +L+EQ VEAGDIWRMCQ KDAP+QDWVKLAVNRARA
Sbjct: 421 YGSHDKTFQIPANGVVRVTDAAGTVLIEQQVEAGDIWRMCQTKDAPVQDWVKLAVNRARA 480

Query: 480 TNTPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTI 539
           TNTPAVFWLD ARAHDAQ+I KVE+YLK++DT+GLDIR+++PVEAT+FS+ RIR GKDTI
Sbjct: 481 TNTPAVFWLDAARAHDAQIIKKVEQYLKNHDTTGLDIRVMTPVEATKFSIERIRAGKDTI 540

Query: 540 SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYL 599
           SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLM+GGG+FETGAGGSAPKHVQQ +EEG+L
Sbjct: 541 SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMFETGAGGSAPKHVQQLVEEGFL 600

Query: 600 RWDSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGS 659
           RWDSLGEFLALAASLEHL +AY NPKA VLA TLDQATGK LDN+KSPARKVG IDNRGS
Sbjct: 601 RWDSLGEFLALAASLEHLSSAYHNPKAQVLAKTLDQATGKFLDNDKSPARKVGGIDNRGS 660

Query: 660 HFYLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPN 719
           HFYLALYWA+ALAAQTED  LQAQF G+AKAL +NE KIV ELAAAQGKPVDI GYY PN
Sbjct: 661 HFYLALYWAEALAAQTEDAALQAQFAGVAKALAENEAKIVEELAAAQGKPVDIGGYYRPN 720

Query: 720 TDLTSKAIRPSATFNAALAPLA 741
            +LTSKA+RPSAT N  +  +A
Sbjct: 721 VELTSKAMRPSATLNKIVDAIA 742


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: 1549
Number of extensions: 50
Number of successful extensions: 2
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: 742
Length adjustment: 40
Effective length of query: 701
Effective length of database: 702
Effective search space:   492102
Effective search space used:   492102
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 BPHYT_RS20300 BPHYT_RS20300 (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.9483.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 1373.5   5.3          0 1373.3   5.3    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS20300  BPHYT_RS20300 isocitrate dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS20300  BPHYT_RS20300 isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1373.3   5.3         0         0       1     742 [.       1     741 [.       1     742 [] 1.00

  Alignments for each domain:
  == domain 1  score: 1373.3 bits;  conditional E-value: 0
                                TIGR00178   1 mstekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalae 70 
                                              mst+ +kiiytltdeap+latysllpivkaf+ s+ + vetrdislagri+a fp+yl+ eqk +d+lae
  lcl|FitnessBrowser__BFirm:BPHYT_RS20300   1 MSTP-PKIIYTLTDEAPALATYSLLPIVKAFTRSSDVIVETRDISLAGRIIAAFPDYLSAEQKGPDDLAE 69 
                                              7787.9**************************************************************** PP

                                TIGR00178  71 lGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvl 140
                                              lG l++ pean+iklpnisasvpqlkaai el+d+Gy+lp yp+ ++td+ekd+kary+kikGsavnpvl
  lcl|FitnessBrowser__BFirm:BPHYT_RS20300  70 LGGLSTRPEANVIKLPNISASVPQLKAAITELRDQGYKLPAYPDVANTDAEKDVKARYDKIKGSAVNPVL 139
                                              ********************************************************************** PP

                                TIGR00178 141 reGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGket 210
                                              reGnsdrrapl+vk+yarkhphkmG+wsadskshvahm+ gdfy+seks+l++aa +vkiel a dG++t
  lcl|FitnessBrowser__BFirm:BPHYT_RS20300 140 REGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMSGGDFYGSEKSALIGAAGSVKIELTATDGSKT 209
                                              ********************************************************************** PP

                                TIGR00178 211 vlkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdv 280
                                              vlk+k+ +++ge+id+svlsk+al+ f+e+ei+dak++gvl+s+hlkatmmkvsdpi+fGhvv+vfykdv
  lcl|FitnessBrowser__BFirm:BPHYT_RS20300 210 VLKEKTAVQAGEIIDASVLSKNALRSFIEAEIADAKAKGVLFSVHLKATMMKVSDPIIFGHVVSVFYKDV 279
                                              ********************************************************************** PP

                                TIGR00178 281 fakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvi 350
                                              ++kha+ l q+G++ +nG++dlya+++ lpa     iead+++ ye+rp+lamv+sdkGit lhvpsdvi
  lcl|FitnessBrowser__BFirm:BPHYT_RS20300 280 LTKHADALAQAGFNPNNGIGDLYARLKDLPAETVAAIEADIKAQYEQRPQLAMVNSDKGITSLHVPSDVI 349
                                              ********************************************************************** PP

                                TIGR00178 351 vdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkae 420
                                              vdasmpamir+sGkm+g+dg l+d+kavipd++yagvyqaviedckk+Gafdp tmGtvpnvGlmaq ae
  lcl|FitnessBrowser__BFirm:BPHYT_RS20300 350 VDASMPAMIRESGKMWGADGALHDAKAVIPDRCYAGVYQAVIEDCKKHGAFDPVTMGTVPNVGLMAQAAE 419
                                              ********************************************************************** PP

                                TIGR00178 421 eyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwl 490
                                              eyGshdktf+i+a+Gvvrv+d+ G vl+e++veagdiwrmcq kdap+qdwvklav+rar+++tpavfwl
  lcl|FitnessBrowser__BFirm:BPHYT_RS20300 420 EYGSHDKTFQIPANGVVRVTDAAGTVLIEQQVEAGDIWRMCQTKDAPVQDWVKLAVNRARATNTPAVFWL 489
                                              ********************************************************************** PP

                                TIGR00178 491 dperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpile 560
                                              d +rahd+++ikkve+ylk+hdt+Gldi+++ pv+at+fs+erir G+dtisvtGnvlrdyltdlfpi+e
  lcl|FitnessBrowser__BFirm:BPHYT_RS20300 490 DAARAHDAQIIKKVEQYLKNHDTTGLDIRVMTPVEATKFSIERIRAGKDTISVTGNVLRDYLTDLFPIME 559
                                              ********************************************************************** PP

                                TIGR00178 561 lGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehvavktgnekakv 630
                                              lGtsakmls+vplmaGGG+fetGaGGsapkhvqql+ee++lrwdslGeflalaasleh++ ++ n+ka+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS20300 560 LGTSAKMLSIVPLMAGGGMFETGAGGSAPKHVQQLVEEGFLRWDSLGEFLALAASLEHLSSAYHNPKAQV 629
                                              ********************************************************************** PP

                                TIGR00178 631 ladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaealtkneeki 700
                                              la+tld+atgk+ld++ksp+rkvG +dnrgs+fyla ywa++laaqted+ l+a+fa+va+al++ne+ki
  lcl|FitnessBrowser__BFirm:BPHYT_RS20300 630 LAKTLDQATGKFLDNDKSPARKVGGIDNRGSHFYLALYWAEALAAQTEDAALQAQFAGVAKALAENEAKI 699
                                              ********************************************************************** PP

                                TIGR00178 701 vaelaavqGeavdlgGyyapdtdlttkvlrpsatfnaileal 742
                                              v+elaa+qG++vd+gGyy p+ +lt+k++rpsat+n+i++a+
  lcl|FitnessBrowser__BFirm:BPHYT_RS20300 700 VEELAAAQGKPVDIGGYYRPNVELTSKAMRPSATLNKIVDAI 741
                                              ****************************************98 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 11.78
//
[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:

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:

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:

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 preprint 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