GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Azospirillum brasilense Sp245

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate AZOBR_RS17090 AZOBR_RS17090 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS17090 AZOBR_RS17090 bifunctional
           aconitate hydratase 2/2-methylisocitrate dehydratase
          Length = 861

 Score = 1256 bits (3251), Expect = 0.0
 Identities = 628/862 (72%), Positives = 720/862 (83%), Gaps = 6/862 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           +LE YR+HVAERAA GI   PL A Q   LV+LL NPP GEE FL+DL+T+RVP GVD+A
Sbjct: 1   VLEAYRQHVAERAALGIPALPLSAKQTEELVDLLLNPPQGEEAFLVDLITHRVPAGVDDA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           A VKA FLA++AKG   SPL++  KA ELLGTM GG+NI PLID L DA+    AA  L 
Sbjct: 61  AKVKAAFLASLAKGNETSPLISKVKATELLGTMLGGFNIKPLIDLLGDAECGEAAAAGLK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
            TLLMFD F+DV+E A  GN  AK V+QSWADAEWF +RP +   LT+T+FKV+GETNTD
Sbjct: 121 TTLLMFDYFHDVKELADKGNANAKAVIQSWADAEWFTSRPEVPASLTLTIFKVSGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLKN R GI P+  GV GPIKQ+E L+ KG  +AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNPRPGIVPEDAGVRGPIKQLEDLKAKGNLVAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLW+ G+DIP+VPNKR GG+CLG KIAPIF+NTMEDAGALPIE+DVS 
Sbjct: 241 GTGSSRKSATNSVLWWTGEDIPYVPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDVSQ 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           +  GD +++ PY+G+   +  G ++A F +K+DV+ DEVRAGGRIPLIIGRGLT +AREA
Sbjct: 301 METGDTVELRPYEGKALKN--GAVIAEFTVKSDVIFDEVRAGGRIPLIIGRGLTARAREA 358

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LGL  S +FR      +S +GF+LAQKMVGRA G+   +G+RPG YCEPKMT+VGSQDTT
Sbjct: 359 LGLAPSTLFRLPSSPVDSGKGFTLAQKMVGRAVGLPEGQGVRPGTYCEPKMTTVGSQDTT 418

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGFSADLVMQSFCHTAAYPK VDV TH  LP FI  RGGV+LRPGDG
Sbjct: 419 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKLVDVKTHRELPTFISTRGGVALRPGDG 478

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           VIHSWLNR+L+PDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 479 VIHSWLNRLLMPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 538

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           G +QPG+TLRDLV+AIPLYAI+QGLLTVEKKGKKNIFSGRILEIEGLP+LKVEQAFEL+D
Sbjct: 539 GALQPGVTLRDLVNAIPLYAIRQGLLTVEKKGKKNIFSGRILEIEGLPELKVEQAFELSD 598

Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
           ASAERSAA CT++LNKEPIIEY+ SNI L+KWMIA GY D RTL RRI+ ME W+ANP L
Sbjct: 599 ASAERSAAACTVRLNKEPIIEYMRSNITLMKWMIANGYEDARTLGRRIKAMEDWIANPSL 658

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
           LE DADAEYAAVIDIDLADIKEPI+  PNDPDD + LS V G+KIDEVFIGSCMTNIGHF
Sbjct: 659 LEPDADAEYAAVIDIDLADIKEPIVACPNDPDDVKLLSEVAGDKIDEVFIGSCMTNIGHF 718

Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAAGK+LD  K  +PTRLW+APPT+MDA  LTEEGYY V GKSGAR+E+PGCSLCMGNQA
Sbjct: 719 RAAGKILDG-KTDIPTRLWIAPPTKMDAQILTEEGYYGVLGKSGARMEMPGCSLCMGNQA 777

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           ++  G+T +STSTRNFPNRLG    V+L SAEL+AVAAL+GKLPTP EY   V+ V++ A
Sbjct: 778 QIRKGSTAISTSTRNFPNRLGIDTRVYLGSAELSAVAALLGKLPTPAEYLEQVSVVNQKA 837

Query: 838 VDTYRYLNFNQLSQYTEKADGV 859
            D YRY+NF+Q+ ++ + AD V
Sbjct: 838 GDIYRYMNFDQIKEFQDVADTV 859


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: 2064
Number of extensions: 73
Number of successful extensions: 4
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: 861
Length adjustment: 42
Effective length of query: 823
Effective length of database: 819
Effective search space:   674037
Effective search space used:   674037
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 AZOBR_RS17090 AZOBR_RS17090 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase)
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.12623.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 1489.8   0.0          0 1489.6   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS17090  AZOBR_RS17090 bifunctional aconi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS17090  AZOBR_RS17090 bifunctional aconitate hydratase 2/2-methylisocitrate dehydra
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1489.6   0.0         0         0       1     844 []       1     854 [.       1     854 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1489.6 bits;  conditional E-value: 0
                                 TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagfla 69 
                                               +le+yr+hvaeraa+gi+ lpl akq+++lv+ll n+p++ee+fl++l+++rvp gvd+aa+vka fla
  lcl|FitnessBrowser__azobra:AZOBR_RS17090   1 VLEAYRQHVAERAALGIPALPLSAKQTEELVDLLLNPPQGEEAFLVDLITHRVPAGVDDAAKVKAAFLA 69 
                                               69******************************************************************* PP

                                 TIGR00117  70 aiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveels 138
                                               ++akg+ +splis  +a+ellgtmlgg+n++pli++l   d++  +aaa  l++tll+fd f+dv+el+
  lcl|FitnessBrowser__azobra:AZOBR_RS17090  70 SLAKGNETSPLISKVKATELLGTMLGGFNIKPLIDLLG--DAECGEAAAAGLKTTLLMFDYFHDVKELA 136
                                               *************************************9..****************************9 PP

                                 TIGR00117 139 kt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknk 206
                                               +  n+ ak v++swa+aewf  ++e++  +t t+fkv+getntddlspapda++rpdiplhalamlkn 
  lcl|FitnessBrowser__azobra:AZOBR_RS17090 137 DKgNANAKAVIQSWADAEWFTSRPEVPASLTLTIFKVSGETNTDDLSPAPDAWSRPDIPLHALAMLKNP 205
                                               988****************************************************************** PP

                                 TIGR00117 207 ieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvl 265
                                               +++i +          ++++lk kg  vayvgdvvgtgssrksatnsvlw+ g+dip+vpnkr gg++l
  lcl|FitnessBrowser__azobra:AZOBR_RS17090 206 RPGIVPedagvrgpikQLEDLKAKGNLVAYVGDVVGTGSSRKSATNSVLWWTGEDIPYVPNKRFGGVCL 274
                                               ****9999************************************************************* PP

                                 TIGR00117 266 ggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevraggr 334
                                               g kiapif+nt+ed+galpie dv+++++gd +++ py+g+   k++ v+a f +k+++++devraggr
  lcl|FitnessBrowser__azobra:AZOBR_RS17090 275 GSKIAPIFYNTMEDAGALPIELDVSQMETGDTVELRPYEGKAL-KNGAVIAEFTVKSDVIFDEVRAGGR 342
                                               *****************************************75.5569********************* PP

                                 TIGR00117 335 ipliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkacgv...kgirpgtycepkvtt 400
                                               ipliigrglt +arealgl++s +f+ +++p +s+kgftlaqk+vg+a g+   +g+rpgtycepk+tt
  lcl|FitnessBrowser__azobra:AZOBR_RS17090 343 IPLIIGRGLTARAREALGLAPSTLFRLPSSPVDSGKGFTLAQKMVGRAVGLpegQGVRPGTYCEPKMTT 411
                                               **************************************************87669************** PP

                                 TIGR00117 401 vgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvi 469
                                               vgsqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypk vdvkth++lp fis+rggvalrpgdgvi
  lcl|FitnessBrowser__azobra:AZOBR_RS17090 412 VGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKLVDVKTHRELPTFISTRGGVALRPGDGVI 480
                                               ********************************************************************* PP

                                 TIGR00117 470 hswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrd 538
                                               hswlnr+l+pdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg lqpg+tlrd
  lcl|FitnessBrowser__azobra:AZOBR_RS17090 481 HSWLNRLLMPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGALQPGVTLRD 549
                                               ********************************************************************* PP

                                 TIGR00117 539 lvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvi 607
                                               lvnaip+yai++glltvekkgk+n+f+grileieglp+lkveqafel+dasaersaa+ct++lnkep+i
  lcl|FitnessBrowser__azobra:AZOBR_RS17090 550 LVNAIPLYAIRQGLLTVEKKGKKNIFSGRILEIEGLPELKVEQAFELSDASAERSAAACTVRLNKEPII 618
                                               ********************************************************************* PP

                                 TIGR00117 608 eylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapn 676
                                               ey++sni l+k+mia+gyed+rtl rri+ame+w+anp+lle+dadaeyaavi+idla+ikepi+a+pn
  lcl|FitnessBrowser__azobra:AZOBR_RS17090 619 EYMRSNITLMKWMIANGYEDARTLGRRIKAMEDWIANPSLLEPDADAEYAAVIDIDLADIKEPIVACPN 687
                                               ********************************************************************* PP

                                 TIGR00117 677 dpddvkllsevagdaidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegyyai 745
                                               dpddvkllsevagd+idevfigscmtnighfraagkil++++++++rlw++ppt+md+q l+eegyy++
  lcl|FitnessBrowser__azobra:AZOBR_RS17090 688 DPDDVKLLSEVAGDKIDEVFIGSCMTNIGHFRAAGKILDGKTDIPTRLWIAPPTKMDAQILTEEGYYGV 756
                                               ********************************************************************* PP

                                 TIGR00117 746 fgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkee 814
                                               +g++gar+e+pgcslcmgnqa+++ g+t +ststrnf+nrlg  ++vylgsael+avaallgk+pt+ e
  lcl|FitnessBrowser__azobra:AZOBR_RS17090 757 LGKSGARMEMPGCSLCMGNQAQIRKGSTAISTSTRNFPNRLGIDTRVYLGSAELSAVAALLGKLPTPAE 825
                                               ********************************************************************* PP

                                 TIGR00117 815 ylalvsekvesakdklyrylnfnelenfee 844
                                               yl+ vs + + a d +yry+nf+++++f++
  lcl|FitnessBrowser__azobra:AZOBR_RS17090 826 YLEQVSVVNQKAGD-IYRYMNFDQIKEFQD 854
                                               ******88877776.************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (861 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: 0.06u 0.04s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 7.86
//
[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