GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS17090
          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.3891918.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 46.88
//
[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:

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