GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS02985
          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.2466759.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 30.21
//
[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