GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Azospirillum brasilense Sp245

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate AZOBR_RS02985 AZOBR_RS02985 aconitate hydratase

Query= SwissProt::P37032
         (891 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS02985 AZOBR_RS02985 aconitate
           hydratase
          Length = 896

 Score = 1201 bits (3107), Expect = 0.0
 Identities = 593/890 (66%), Positives = 706/890 (79%), Gaps = 3/890 (0%)

Query: 4   GQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTK 63
           GQDSL T+  L+V GK+Y+Y+S+K AE+     ++RLPYS+KVLLENLLRFEDG TV+T 
Sbjct: 6   GQDSLKTRRSLSVGGKSYDYFSIKAAEDAGLGDLSRLPYSMKVLLENLLRFEDGRTVSTD 65

Query: 64  DIKAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLS 123
           D+KA+A WLH+K S  EIA+RP RVLMQDFTGVPAV DLAAMR A+  +GG+  KI+PL 
Sbjct: 66  DVKAVAQWLHDKRSDREIAYRPARVLMQDFTGVPAVCDLAAMREAMAALGGDPKKINPLV 125

Query: 124 PVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICH 183
           PVDLVIDHSVMVD F +  A E N ++E ERN ERY FLRWGQKAF NF+VVPPGTGICH
Sbjct: 126 PVDLVIDHSVMVDYFGNPSAFEKNVELEFERNLERYAFLRWGQKAFDNFRVVPPGTGICH 185

Query: 184 QVNLEYLGKTVW-NSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 242
           QVN+EYL + VW +++  G+L AYPDTLVGTDSHTTM+NGLGVLGWGVGGIEAEAAMLGQ
Sbjct: 186 QVNVEYLAQGVWTDTDPAGKLVAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQ 245

Query: 243 PVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADR 302
           P+SMLIPEV+GFKL+G+LKEG TATDLVLTVTQMLRKKGVVGKFVEFYGPGL+ L LADR
Sbjct: 246 PISMLIPEVVGFKLTGRLKEGTTATDLVLTVTQMLRKKGVVGKFVEFYGPGLDHLTLADR 305

Query: 303 ATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVF 362
           ATI NMAPEYGATCG FP+D ETI+YL  TGRD   +A+VEAYA+AQGMW D    +PVF
Sbjct: 306 ATIGNMAPEYGATCGIFPIDAETIRYLTFTGRDADRVAMVEAYARAQGMWRDAGTPDPVF 365

Query: 363 TDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDFQM 422
           TD+L LD+ +VEPSLAGPKRPQD+V LS     F   L+   K ++ +++  VK   + +
Sbjct: 366 TDALELDMTTVEPSLAGPKRPQDRVPLSQAAQSFGTDLVGAFKAEDADRSVPVKGCGYNL 425

Query: 423 KHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRH 482
             G VVIAAITSCTNTSNP+VL+AAGL+A+KA+EKGL+ KPWVK+SLAPGS+VVTDYL  
Sbjct: 426 DQGAVVIAAITSCTNTSNPAVLVAAGLLARKAVEKGLKSKPWVKTSLAPGSQVVTDYLAK 485

Query: 483 AGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHP 542
           AGLQ YLDQLGFN+VGYGCTTCIGNSGPLPD I+  V E +LVV++VLSGNRNFEGRV+P
Sbjct: 486 AGLQPYLDQLGFNIVGYGCTTCIGNSGPLPDPIAAAVEEGNLVVAAVLSGNRNFEGRVNP 545

Query: 543 QVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEV-AKV 601
             RAN+LASPPL VAYAL G    DL+++PIG   +G  VYLKD+WP+N+E+   + A +
Sbjct: 546 HTRANYLASPPLCVAYALAGNMKIDLAKDPIGTGHDGQPVYLKDVWPTNQEVQDAIDASL 605

Query: 602 SGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIKQ 661
           S  MFR  Y  VF+G   W+ IQT+ GQTYEW   STY++ PPFF ++   P+ +  ++ 
Sbjct: 606 SAEMFRSRYGNVFEGPEQWRGIQTAEGQTYEWQAGSTYVKLPPFFADMPKTPDAVSDVRG 665

Query: 662 AYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTF 721
           A  LA+ GDSITTDHISPAGSIK +SPAG YL S  V  +DFNSYG+RRGNHEVMMRGTF
Sbjct: 666 ARALAVLGDSITTDHISPAGSIKKTSPAGEYLLSHQVRPQDFNSYGARRGNHEVMMRGTF 725

Query: 722 ANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWA 781
           ANIRIRNEM  G EGG TR+ P+GE + IY AAMRY +    LV+IAGKEYGTGSSRDWA
Sbjct: 726 ANIRIRNEMLAGVEGGETRHYPSGEQLPIYTAAMRYAQEGVPLVVIAGKEYGTGSSRDWA 785

Query: 782 AKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIE-ISDK 840
           AKGT LLG++AVI ESFERIHRSNL+GMGILPLQFK+G TR  L LDG+E   I+ I   
Sbjct: 786 AKGTKLLGIRAVIAESFERIHRSNLVGMGILPLQFKDGLTRNDLALDGTETFDIDGIEQD 845

Query: 841 LTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKIS 890
           L P   V +TI R DG   ++  L RIDT DE+EYY+NGG+L +VLR ++
Sbjct: 846 LRPRKDVTMTITRADGQTRQVPLLLRIDTVDEVEYYRNGGVLNFVLRNLA 895


Lambda     K      H
   0.316    0.134    0.393 

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: 2142
Number of extensions: 82
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: 891
Length of database: 896
Length adjustment: 43
Effective length of query: 848
Effective length of database: 853
Effective search space:   723344
Effective search space used:   723344
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 (21.6 bits)
S2: 56 (26.2 bits)

Align candidate AZOBR_RS02985 AZOBR_RS02985 (aconitate hydratase)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (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/TIGR01341.hmm
# target sequence database:        /tmp/gapView.15755.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01341  [M=876]
Accession:   TIGR01341
Description: aconitase_1: aconitate hydratase 1
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 1409.9   0.0          0 1409.7   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS02985  AZOBR_RS02985 aconitate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS02985  AZOBR_RS02985 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1409.7   0.0         0         0       2     875 ..      22     894 ..      21     895 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1409.7 bits;  conditional E-value: 0
                                 TIGR01341   2 kvyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparv 69 
                                               ++ y+s+ka+e++ l+++s+lp+s+++lle++lr  dg++++ +dv+a+++w +++ +d+eia++parv
  lcl|FitnessBrowser__azobra:AZOBR_RS02985  22 SYDYFSIKAAEDAgLGDLSRLPYSMKVLLENLLRFEDGRTVSTDDVKAVAQWLHDKRSDREIAYRPARV 90 
                                               789********99789***************************************************** PP

                                 TIGR01341  70 vlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernke 138
                                               ++qdftGvpav dlaa+rea+++lg+dp+kinplvpvdlvidhsv vd++g+ +a+e+nvelefern e
  lcl|FitnessBrowser__azobra:AZOBR_RS02985  91 LMQDFTGVPAVCDLAAMREAMAALGGDPKKINPLVPVDLVIDHSVMVDYFGNPSAFEKNVELEFERNLE 159
                                               ********************************************************************* PP

                                 TIGR01341 139 rykflkwakkafknlkvvppgtGivhqvnleylakvvfe.aekdgellaypdslvGtdshttminGlGv 206
                                               ry+fl+w++kaf n++vvppgtGi+hqvn+eyla+ v++ ++  g+l+aypd+lvGtdshttm+nGlGv
  lcl|FitnessBrowser__azobra:AZOBR_RS02985 160 RYAFLRWGQKAFDNFRVVPPGTGICHQVNVEYLAQGVWTdTDPAGKLVAYPDTLVGTDSHTTMVNGLGV 228
                                               ***********************************999725568************************* PP

                                 TIGR01341 207 lGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGegl 275
                                               lGwGvGGieaeaa+lGqp+s+ +pev+G+kltG+l+eG+tatdlvltvt++lrkkgvvgkfvef+G+gl
  lcl|FitnessBrowser__azobra:AZOBR_RS02985 229 LGWGVGGIEAEAAMLGQPISMLIPEVVGFKLTGRLKEGTTATDLVLTVTQMLRKKGVVGKFVEFYGPGL 297
                                               ********************************************************************* PP

                                 TIGR01341 276 kelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkyt 343
                                               ++l+ladrati nmapeyGat+++fpid++t+ yl  tgrd d+v +ve+y++aq++++d  + +p++t
  lcl|FitnessBrowser__azobra:AZOBR_RS02985 298 DHLTLADRATIGNMAPEYGATCGIFPIDAETIRYLTFTGRDADRVAMVEAYARAQGMWRDaGTPDPVFT 366
                                               ************************************************************66678**** PP

                                 TIGR01341 344 dvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeakekklegkeaelkdgav 412
                                               d +eld+ +ve+s+aGpkrpqdrv+l++  ++f + l      ++       ++  ++g  ++l++gav
  lcl|FitnessBrowser__azobra:AZOBR_RS02985 367 DALELDMTTVEPSLAGPKRPQDRVPLSQAAQSFGTDLVGAFKAED-----ADRSVPVKGCGYNLDQGAV 430
                                               **********************************99986554444.....5566677899********* PP

                                 TIGR01341 413 viaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnl 481
                                               viaaitsctntsnp+vl++aglla+kave Glk kp+vktslapGs+vvtdyla++gl+pyl++lGfn+
  lcl|FitnessBrowser__azobra:AZOBR_RS02985 431 VIAAITSCTNTSNPAVLVAAGLLARKAVEKGLKSKPWVKTSLAPGSQVVTDYLAKAGLQPYLDQLGFNI 499
                                               ********************************************************************* PP

                                 TIGR01341 482 vGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvd 550
                                               vGyGcttciGnsGpl++ ++ a+ e++l+v+avlsGnrnfegr++p ++anylasppl vayalaG+++
  lcl|FitnessBrowser__azobra:AZOBR_RS02985 500 VGYGCTTCIGNSGPLPDPIAAAVEEGNLVVAAVLSGNRNFEGRVNPHTRANYLASPPLCVAYALAGNMK 568
                                               ********************************************************************* PP

                                 TIGR01341 551 idlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyew 619
                                               idl+k+pigt++dG++vylkd+wp+++e++++++ +++ e+f+ +y +v+eg e+w+ ++++++++yew
  lcl|FitnessBrowser__azobra:AZOBR_RS02985 569 IDLAKDPIGTGHDGQPVYLKDVWPTNQEVQDAIDASLSAEMFRSRYGNVFEGPEQWRGIQTAEGQTYEW 637
                                               ********************************************************************* PP

                                 TIGR01341 620 dekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrd 688
                                               +  sty+++ppff ++  +p+ v+d++gar l++lGdsittdhispaGsikk spa++yl  + v ++d
  lcl|FitnessBrowser__azobra:AZOBR_RS02985 638 QAGSTYVKLPPFFADMPKTPDAVSDVRGARALAVLGDSITTDHISPAGSIKKTSPAGEYLLSHQVRPQD 706
                                               ********************************************************************* PP

                                 TIGR01341 689 fnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGke 757
                                               fnsyG+rrGnhevm+rGtfaniri+n+++ g eGg t+++p +e++ +y aam+y +egvplvv+aGke
  lcl|FitnessBrowser__azobra:AZOBR_RS02985 707 FNSYGARRGNHEVMMRGTFANIRIRNEMLAGVEGGETRHYPSGEQLPIYTAAMRYAQEGVPLVVIAGKE 775
                                               ********************************************************************* PP

                                 TIGR01341 758 yGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddi.e 825
                                               yG+GssrdwaakgtkllG++aviaesferihrsnlvgmG+lpl+fk+g +++ l l+g+et d+d+i +
  lcl|FitnessBrowser__azobra:AZOBR_RS02985 776 YGTGSSRDWAAKGTKLLGIRAVIAESFERIHRSNLVGMGILPLQFKDGLTRNDLALDGTETFDIDGIeQ 844
                                               ******************************************************************835 PP

                                 TIGR01341 826 elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkl 875
                                               +l+p+k+vt++++++dg+ + v   lridt  e++y+++gG+l++vlr+l
  lcl|FitnessBrowser__azobra:AZOBR_RS02985 845 DLRPRKDVTMTITRADGQTRQVPLLLRIDTVDEVEYYRNGGVLNFVLRNL 894
                                               8***********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (896 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: 7.91
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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