GapMind for catabolism of small carbon sources

 

Aligments for a candidate for icd in Cupriavidus basilensis 4G11

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate RR42_RS28800 RR42_RS28800 isocitrate dehydrogenase

Query= BRENDA::O53611
         (745 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS28800 RR42_RS28800 isocitrate
           dehydrogenase
          Length = 745

 Score = 1224 bits (3167), Expect = 0.0
 Identities = 604/744 (81%), Positives = 664/744 (89%)

Query: 1   MSAEQPTIIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTE 60
           MS +QPTIIYTLTDEAPLLAT AFLPI+R F  PAGI +  SDISVA RIL EFP++LTE
Sbjct: 1   MSTQQPTIIYTLTDEAPLLATSAFLPIIRTFTAPAGINVTTSDISVAGRILGEFPEFLTE 60

Query: 61  EQRVPDNLAELGRLTQLPDTNIIKLPNISASVPQLVAAIKELQDKGYAVPDYPADPKTDQ 120
            QRVPDNLAELGRLT  PDTNIIKLPNISASV QLV+AIKELQ KGY VPD+P DPKTD 
Sbjct: 61  AQRVPDNLAELGRLTLQPDTNIIKLPNISASVHQLVSAIKELQAKGYKVPDFPEDPKTDA 120

Query: 121 EKAIKERYARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGEWSMASRTHVAHMRH 180
           EKAI++RY++CLGSAVNPVLR+GNSDRRAP AVK YARK+PHSMGEWSMASRTHVAHM+H
Sbjct: 121 EKAIRQRYSKCLGSAVNPVLREGNSDRRAPAAVKNYARKNPHSMGEWSMASRTHVAHMKH 180

Query: 181 GDFYAGEKSMTLDRARNVRMELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEE 240
           GDFY GEKSMTLDRAR+V+MEL+ KSGKTIVLKP+V L DG++IDSMFMSKKALCDFYEE
Sbjct: 181 GDFYHGEKSMTLDRARDVKMELVTKSGKTIVLKPKVSLLDGEIIDSMFMSKKALCDFYEE 240

Query: 241 QMQDAFETGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLS 300
           QM+DA +TGVM SLHVKATMMKVSHPIVFGHAV+IFYK+AF KH +LFD+LGVNVNNGL 
Sbjct: 241 QMEDARKTGVMLSLHVKATMMKVSHPIVFGHAVKIFYKEAFEKHGKLFDELGVNVNNGLV 300

Query: 301 DLYSKIESLPASQRDEIIEDLHRCHEHRPELAMVDSARGISNFHSPSDVIVDASMPAMIR 360
           +LY K+ESLP+S+R+EII D+H CHEHRPELAMVDSA+GISN H+P+DVIVDASMPAMIR
Sbjct: 301 NLYDKLESLPSSKREEIIRDMHACHEHRPELAMVDSAKGISNLHAPNDVIVDASMPAMIR 360

Query: 361 AGGKMYGADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQFDPTTMGTVPNVGLMAQQAE 420
            GGKM+GADG+ KDTKAV PESTF+RIYQEIINFCKTNG FDP TMGTVPNVGLMAQQAE
Sbjct: 361 IGGKMWGADGRPKDTKAVIPESTFARIYQEIINFCKTNGNFDPVTMGTVPNVGLMAQQAE 420

Query: 421 EYGSHDKTFEIPEDGVANIVDVATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRA 480
           EYGSHDKTFE+PE G A IVD+ATGEVLL +NVE GDIWRMC VKDAPIRDWVKLAVTRA
Sbjct: 421 EYGSHDKTFEVPEAGEARIVDIATGEVLLVQNVEEGDIWRMCQVKDAPIRDWVKLAVTRA 480

Query: 481 RISGMPVLFWLDPYRPHENELIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLD 540
           R SGMP +FWLDPYRPHE E+IKKV+TYLKDHDT GLDIQIMSQVR+MRYT ER++RGLD
Sbjct: 481 RNSGMPAIFWLDPYRPHEAEMIKKVETYLKDHDTTGLDIQIMSQVRAMRYTLERVIRGLD 540

Query: 541 TIAATGNILRDYLTDLFPILELGTSAKMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEEN 600
           TI+ TGNILRDYLTDLFPI+ELGTSAKMLS+VPLMAGGGMYETGAGGSAPKHVKQLVEEN
Sbjct: 541 TISVTGNILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMYETGAGGSAPKHVKQLVEEN 600

Query: 601 HLRWDSLGEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDNDKSPSRKTGELDNR 660
           HLRWDSLGEFLAL    E++GIKT NE+AK+L KTLDAA GKLLDN+K+PS KTG+LDNR
Sbjct: 601 HLRWDSLGEFLALAVSLEELGIKTSNEKAKVLAKTLDAATGKLLDNNKNPSPKTGQLDNR 660

Query: 661 GSQFYLAMYWAQELAAQTDDQQLAEHFASLADVLTKNEDVIVRELTEVQGEPVDIGGYYA 720
           GSQFYLAMYWAQELAAQTDD  LA  FA LA  LT NE VIV EL+ VQG+  DIGGYY 
Sbjct: 661 GSQFYLAMYWAQELAAQTDDAALAAQFAPLAKQLTDNEQVIVGELSAVQGKQADIGGYYK 720

Query: 721 PDSDMTTAVMRPSKTFNAALEAVQ 744
           PD      VMRPSKT NAAL AV+
Sbjct: 721 PDFAKLDIVMRPSKTLNAALAAVK 744


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: 1587
Number of extensions: 41
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: 745
Length adjustment: 40
Effective length of query: 705
Effective length of database: 705
Effective search space:   497025
Effective search space used:   497025
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 RR42_RS28800 RR42_RS28800 (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.17350.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 1381.3   0.4          0 1381.2   0.4    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS28800  RR42_RS28800 isocitrate dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS28800  RR42_RS28800 isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1381.2   0.4         0         0       1     743 [.       1     744 [.       1     745 [] 1.00

  Alignments for each domain:
  == domain 1  score: 1381.2 bits;  conditional E-value: 0
                                 TIGR00178   1 mstekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddala 69 
                                               mst++++iiytltdeapllat ++lpi+++f+a+aGi+v t+dis+agril efpe+lte q+v+d+la
  lcl|FitnessBrowser__Cup4G11:RR42_RS28800   1 MSTQQPTIIYTLTDEAPLLATSAFLPIIRTFTAPAGINVTTSDISVAGRILGEFPEFLTEAQRVPDNLA 69 
                                               9******************************************************************** PP

                                 TIGR00178  70 elGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnp 138
                                               elG+l+  p++niiklpnisasv ql++aikelq+kGy++pd+pe+pktd+ek+i++ry+k++Gsavnp
  lcl|FitnessBrowser__Cup4G11:RR42_RS28800  70 ELGRLTLQPDTNIIKLPNISASVHQLVSAIKELQAKGYKVPDFPEDPKTDAEKAIRQRYSKCLGSAVNP 138
                                               ********************************************************************* PP

                                 TIGR00178 139 vlreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdG 207
                                               vlreGnsdrrap+avk+yark+ph+mGews++s++hvahm++gdfy++eks++ld+a++vk+el++k+G
  lcl|FitnessBrowser__Cup4G11:RR42_RS28800 139 VLREGNSDRRAPAAVKNYARKNPHSMGEWSMASRTHVAHMKHGDFYHGEKSMTLDRARDVKMELVTKSG 207
                                               ********************************************************************* PP

                                 TIGR00178 208 ketvlkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvf 276
                                               k++vlk+k++lldge+ids+++skkal++f+ee++eda+++gv+lslh+katmmkvs+pivfGh+v++f
  lcl|FitnessBrowser__Cup4G11:RR42_RS28800 208 KTIVLKPKVSLLDGEIIDSMFMSKKALCDFYEEQMEDARKTGVMLSLHVKATMMKVSHPIVFGHAVKIF 276
                                               ********************************************************************* PP

                                 TIGR00178 277 ykdvfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhv 345
                                               yk++f kh++l+++lG++v+nGl +ly k+eslp++k+eei+ d+++++e+rpelamvds+kGi+nlh+
  lcl|FitnessBrowser__Cup4G11:RR42_RS28800 277 YKEAFEKHGKLFDELGVNVNNGLVNLYDKLESLPSSKREEIIRDMHACHEHRPELAMVDSAKGISNLHA 345
                                               ********************************************************************* PP

                                 TIGR00178 346 psdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGl 414
                                               p dvivdasmpamir +Gkm+g+dg+ kdtkavip+s++a++yq++i++ck+nG+fdp tmGtvpnvGl
  lcl|FitnessBrowser__Cup4G11:RR42_RS28800 346 PNDVIVDASMPAMIRIGGKMWGADGRPKDTKAVIPESTFARIYQEIINFCKTNGNFDPVTMGTVPNVGL 414
                                               ********************************************************************* PP

                                 TIGR00178 415 maqkaeeyGshdktfeieadGvvrvvd.ssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarls 482
                                               maq+aeeyGshdktfe++++G +r+vd ++Gevll ++ve+gdiwrmcqvkdapi+dwvklavtrar s
  lcl|FitnessBrowser__Cup4G11:RR42_RS28800 415 MAQQAEEYGSHDKTFEVPEAGEARIVDiATGEVLLVQNVEEGDIWRMCQVKDAPIRDWVKLAVTRARNS 483
                                               ***************************99**************************************** PP

                                 TIGR00178 483 gtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdy 551
                                               g+pa+fwldp+r+h++e+ikkve+ylkdhdt+Gldiqi+s+v+a+r++ler+ rG dtisvtGn+lrdy
  lcl|FitnessBrowser__Cup4G11:RR42_RS28800 484 GMPAIFWLDPYRPHEAEMIKKVETYLKDHDTTGLDIQIMSQVRAMRYTLERVIRGLDTISVTGNILRDY 552
                                               ********************************************************************* PP

                                 TIGR00178 552 ltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehva 620
                                               ltdlfpi+elGtsakmls+vplmaGGG++etGaGGsapkhv+ql+eenhlrwdslGeflala sle+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS28800 553 LTDLFPIMELGTSAKMLSIVPLMAGGGMYETGAGGSAPKHVKQLVEENHLRWDSLGEFLALAVSLEELG 621
                                               ********************************************************************* PP

                                 TIGR00178 621 vktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasv 689
                                               +kt nekakvla+tldaatgklld++k ps k+G+ldnrgs+fyla+ywaqelaaqt+d+ laa+fa++
  lcl|FitnessBrowser__Cup4G11:RR42_RS28800 622 IKTSNEKAKVLAKTLDAATGKLLDNNKNPSPKTGQLDNRGSQFYLAMYWAQELAAQTDDAALAAQFAPL 690
                                               ********************************************************************* PP

                                 TIGR00178 690 aealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnailealk 743
                                               a+ lt+ne++iv+el+avqG+  d+gGyy+pd  +++ v+rps+t+na+l+a+k
  lcl|FitnessBrowser__Cup4G11:RR42_RS28800 691 AKQLTDNEQVIVGELSAVQGKQADIGGYYKPDFAKLDIVMRPSKTLNAALAAVK 744
                                               ***************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (745 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: 8.76
//
[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