GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Dyella japonica UNC79MFTsu3.2

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate N515DRAFT_1420 N515DRAFT_1420 aconitase

Query= BRENDA::P36683
         (865 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 N515DRAFT_1420
           aconitase
          Length = 863

 Score = 1260 bits (3261), Expect = 0.0
 Identities = 627/864 (72%), Positives = 734/864 (84%), Gaps = 8/864 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           ML  YR+HVAERAA GI   PL A Q A L+ELLKNPPAGEE FL+DL++NRVP GVD+A
Sbjct: 1   MLNAYRQHVAERAALGIPALPLTAQQTADLIELLKNPPAGEEAFLVDLISNRVPAGVDDA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           A VKA +LAA+A G+   PLL+  KA ELLGTM GGYNIHPLI+ LDDA++  IAA AL 
Sbjct: 61  AKVKASYLAAVAFGKEPCPLLSRAKATELLGTMLGGYNIHPLIELLDDAQVGGIAADALK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
            TLLMFD+F+DV+EKA  GN  AK V+QSWADAEWF +RP +   LT+TVFKV GETNTD
Sbjct: 121 KTLLMFDSFHDVKEKADKGNANAKAVLQSWADAEWFTSRPEVPASLTITVFKVPGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREG--IEPDQPGVVGPIKQIEALQQKGFPLAYVGD 238
           DLSPAPDA +RPDIPLHALAMLKN REG   +P++ G  GPI+QI+ L ++G  +AYVGD
Sbjct: 181 DLSPAPDATTRPDIPLHALAMLKNKREGAPFQPEEDGKRGPIQQIQDLARQGHLVAYVGD 240

Query: 239 VVGTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298
           VVGTGSSRKSATNSVLW+ G+DIP +PNKR GG+CLG KIAPIF+NTMEDAGALPIE+DV
Sbjct: 241 VVGTGSSRKSATNSVLWWTGEDIPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDV 300

Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358
           S ++MGDV+++ PY+G+   +  GE++A F++K+DVL DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 SQMDMGDVVELRPYEGKALKN--GEVIAEFQVKSDVLFDEVRAGGRIPLIIGRGLTAKAR 358

Query: 359 EALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415
           EALGL  S +FR  ++ A++ +G++LAQKMVGRACG+   +G+RPG YCEPKMTSVGSQD
Sbjct: 359 EALGLAPSTLFRLPQNPADTGKGYTLAQKMVGRACGLAEGEGVRPGTYCEPKMTSVGSQD 418

Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPG 475
           TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV THH LP FI  RGG+SLRPG
Sbjct: 419 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHELPAFISTRGGISLRPG 478

Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535
           DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR
Sbjct: 479 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 538

Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595
           FKG++QPG+TLRDLV+AIPLYAIKQGLLTV K+GK+NIFSGRILEIEGLP+LKVEQAFEL
Sbjct: 539 FKGELQPGVTLRDLVNAIPLYAIKQGLLTVAKQGKQNIFSGRILEIEGLPNLKVEQAFEL 598

Query: 596 TDASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANP 655
           +DASAERSAAGCT++L++ PIIEYLNSNI LLK+MIA+GY D R+L RRI+ ME+WLANP
Sbjct: 599 SDASAERSAAGCTVRLDQAPIIEYLNSNITLLKYMIAQGYQDARSLSRRIKKMEEWLANP 658

Query: 656 ELLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIG 715
           +LLE DADAEYAAVI+IDLAD+ EPI+  PNDPDD + LS V G KIDEVFIGSCMTNIG
Sbjct: 659 QLLEPDADAEYAAVIEIDLADVHEPIVACPNDPDDVKSLSDVAGAKIDEVFIGSCMTNIG 718

Query: 716 HFRAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775
           HFRAA KLL+  K  +PTRLWVAPPT+MD  QLTEEG+Y V G +GAR+E+PGCSLCMGN
Sbjct: 719 HFRAASKLLEG-KRDIPTRLWVAPPTKMDQQQLTEEGHYGVLGTAGARMEMPGCSLCMGN 777

Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835
           QA+V +GATV+STSTRNFPNRLG   NV+L SAELAA+ + +G++PT EEY   +  ++ 
Sbjct: 778 QAQVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGRIPTKEEYMADIGVINA 837

Query: 836 TAVDTYRYLNFNQLSQYTEKADGV 859
                YRY+NF+Q++ + + AD V
Sbjct: 838 NGEKIYRYMNFDQIADFKQVADTV 861


Lambda     K      H
   0.317    0.136    0.400 

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: 2066
Number of extensions: 79
Number of successful extensions: 5
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: 865
Length of database: 863
Length adjustment: 42
Effective length of query: 823
Effective length of database: 821
Effective search space:   675683
Effective search space used:   675683
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: 56 (26.2 bits)

Align candidate N515DRAFT_1420 N515DRAFT_1420 (aconitase)
to HMM TIGR00117 (acnB: aconitate hydratase 2 (EC 4.2.1.3))

# 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/TIGR00117.hmm
# target sequence database:        /tmp/gapView.23537.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00117  [M=844]
Accession:   TIGR00117
Description: acnB: aconitate hydratase 2
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 1510.9   0.0          0 1510.7   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420  N515DRAFT_1420 aconitase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_1420  N515DRAFT_1420 aconitase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1510.7   0.0         0         0       1     843 [.       1     855 [.       1     856 [. 0.98

  Alignments for each domain:
  == domain 1  score: 1510.7 bits;  conditional E-value: 0
                                    TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkag 66 
                                                  +l++yr+hvaeraa+gi+ lpl a+q+a+l+ellkn+p++ee+fl++l+ +rvp gvd+aa+vka 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420   1 MLNAYRQHVAERAALGIPALPLTAQQTADLIELLKNPPAGEEAFLVDLISNRVPAGVDDAAKVKAS 66 
                                                  799*************************************************************** PP

                                    TIGR00117  67 flaaiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafd 132
                                                  +laa+a g+  +pl+s  +a+ellgtmlggyn++plie+l+  d+++  +aa al+ktll+fd+f+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420  67 YLAAVAFGKEPCPLLSRAKATELLGTMLGGYNIHPLIELLD--DAQVGGIAADALKKTLLMFDSFH 130
                                                  *****************************************..*********************** PP

                                    TIGR00117 133 dveelskt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdipl 197
                                                  dv+e+++  n+ ak vl+swa+aewf  ++e++  +t+tvfkv+getntddlspapda+trpdipl
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 131 DVKEKADKgNANAKAVLQSWADAEWFTSRPEVPASLTITVFKVPGETNTDDLSPAPDATTRPDIPL 196
                                                  *****9988********************************************************* PP

                                    TIGR00117 198 halamlknkieeieq............rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkd 251
                                                  halamlknk+e+               +i++l ++g+ vayvgdvvgtgssrksatnsvlw+ g+d
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 197 HALAMLKNKREGAPFqpeedgkrgpiqQIQDLARQGHLVAYVGDVVGTGSSRKSATNSVLWWTGED 262
                                                  **********99755678999********************************************* PP

                                    TIGR00117 252 ipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnketevvat 317
                                                  ipf+pnkr gg++lg kiapif+nt+ed+galpie dv+++++gdv+++ py+g+   k++ev+a 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 263 IPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDVSQMDMGDVVELRPYEGKAL-KNGEVIAE 327
                                                  *******************************************************75.566***** PP

                                    TIGR00117 318 fklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkac 383
                                                  f++k+++l+devraggripliigrglt karealgl++s +f+ +++pa+++kg+tlaqk+vg+ac
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 328 FQVKSDVLFDEVRAGGRIPLIIGRGLTAKAREALGLAPSTLFRLPQNPADTGKGYTLAQKMVGRAC 393
                                                  ****************************************************************** PP

                                    TIGR00117 384 gv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkt 446
                                                  g+   +g+rpgtycepk+t+vgsqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypkpvdvkt
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 394 GLaegEGVRPGTYCEPKMTSVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKT 459
                                                  *855569*********************************************************** PP

                                    TIGR00117 447 hktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatg 512
                                                  h++lp fis+rgg++lrpgdgvihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatg
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 460 HHELPAFISTRGGISLRPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATG 525
                                                  ****************************************************************** PP

                                    TIGR00117 513 vmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlk 578
                                                  vmpldmpesvlvrfkgelqpg+tlrdlvnaip+yaik+glltv k+gk n+f+grileieglp+lk
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 526 VMPLDMPESVLVRFKGELQPGVTLRDLVNAIPLYAIKQGLLTVAKQGKQNIFSGRILEIEGLPNLK 591
                                                  ****************************************************************** PP

                                    TIGR00117 579 veqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlan 644
                                                  veqafel+dasaersaagct++l++ p+ieyl+sni llk mia+gy+d+r+l rri++me+wlan
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 592 VEQAFELSDASAERSAAGCTVRLDQAPIIEYLNSNITLLKYMIAQGYQDARSLSRRIKKMEEWLAN 657
                                                  ****************************************************************** PP

                                    TIGR00117 645 pelleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraa 710
                                                  p+lle+dadaeyaavieidla+++epi+a+pndpddvk+ls+vag +idevfigscmtnighfraa
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 658 PQLLEPDADAEYAAVIEIDLADVHEPIVACPNDPDDVKSLSDVAGAKIDEVFIGSCMTNIGHFRAA 723
                                                  ****************************************************************** PP

                                    TIGR00117 711 gkileaaktvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfs 776
                                                  +k+le+++++++rlwv+ppt+md+qql+eeg y+++g+agar+e+pgcslcmgnqa+v++gatv+s
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 724 SKLLEGKRDIPTRLWVAPPTKMDQQQLTEEGHYGVLGTAGARMEMPGCSLCMGNQAQVREGATVMS 789
                                                  ****************************************************************** PP

                                    TIGR00117 777 tstrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenf 842
                                                  tstrnf+nrlgk ++vylgsaelaa+++ lg+iptkeey+a +   ++++ +k+yry+nf+++ +f
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 790 TSTRNFPNRLGKNTNVYLGSAELAAICSRLGRIPTKEEYMADIGV-INANGEKIYRYMNFDQIADF 854
                                                  *****************************************9975.6667778***********99 PP

                                    TIGR00117 843 e 843
                                                  +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 855 K 855
                                                  7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (863 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: 0.07u 0.02s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.33
//
[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