GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_3296 Ga0059261_3296 aconitate hydratase 1

Query= SwissProt::P37032
         (891 letters)



>FitnessBrowser__Korea:Ga0059261_3296
          Length = 890

 Score = 1149 bits (2972), Expect = 0.0
 Identities = 585/891 (65%), Positives = 688/891 (77%), Gaps = 8/891 (0%)

Query: 3   VGQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTT 62
           +GQDSL T+  LTV GK+Y+YYSL++A  K    ++RLP+S+KVLLEN+LRFEDG TVT 
Sbjct: 4   IGQDSLGTRETLTVGGKSYSYYSLEKAAAK-LGDVSRLPFSMKVLLENMLRFEDGVTVTP 62

Query: 63  KDIKAIADWLHNKTS-QHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISP 121
           +D +AI DW  N  + + EI +RP RVLMQDFTGVP VVDLAAMR AI K+GG+A KI+P
Sbjct: 63  EDAQAIVDWQKNPNAPEREIQYRPARVLMQDFTGVPCVVDLAAMRDAITKLGGDAAKINP 122

Query: 122 LSPVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGI 181
             PV LVIDHSVMVD+F +  A E N ++E +RN ERY+FL+WG K+  NF+VVPPGTGI
Sbjct: 123 QVPVHLVIDHSVMVDEFGTPKAFEENVELEYQRNMERYDFLKWGSKSLDNFKVVPPGTGI 182

Query: 182 CHQVNLEYLGKTVWNSEN-DGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAML 240
           CHQVNLEY+   +W+S   DG   AYPDTLVGTDSHTTM+NGLGVLGWGVGGIEAEAAML
Sbjct: 183 CHQVNLEYIADAIWSSTAADGTTVAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAML 242

Query: 241 GQPVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLA 300
           GQPVSMLIPEV+GFKL+GKL+EGITATDLVLTVTQMLR +GVVG+FVEF+GPGL  + LA
Sbjct: 243 GQPVSMLIPEVVGFKLTGKLQEGITATDLVLTVTQMLRARGVVGRFVEFFGPGLATMTLA 302

Query: 301 DRATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEP 360
           DRATI+NMAPEYGATCGFF +D +T+ Y+ LTGRD  T+ LVEAY KAQGMW   D  +P
Sbjct: 303 DRATIANMAPEYGATCGFFGIDDKTLDYMRLTGRDDDTVTLVEAYCKAQGMWRYDDMADP 362

Query: 361 VFTDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDF 420
           +FTD+L LD+ +V  SLAGPKRPQD+V+L+ +   FN  L +V   KE     AV+ KD 
Sbjct: 363 IFTDTLELDMATVTASLAGPKRPQDRVSLNKVDEVFNGDLFKV-YGKENGHRVAVEGKDH 421

Query: 421 QMKHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYL 480
            +  G VVIAAITSCTNTSNPSVL+AAGLVA+KA  KGL RKPWVK+SLAPGS+VVTDYL
Sbjct: 422 DIGDGDVVIAAITSCTNTSNPSVLIAAGLVARKARAKGLTRKPWVKTSLAPGSQVVTDYL 481

Query: 481 RHAGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRV 540
             AGL   LD +GFNLVGYGCTTCIGNSGPL   IS  +  +D+V +SVLSGNRNFEGRV
Sbjct: 482 NKAGLSEDLDAIGFNLVGYGCTTCIGNSGPLAQPISDAINGNDIVAASVLSGNRNFEGRV 541

Query: 541 HPQVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEV-A 599
            P VRAN+LASPPLVVAYAL GT   D+   PIG+  +G  VYLKDIWP+NEE+   + A
Sbjct: 542 SPDVRANFLASPPLVVAYALKGTVTEDMIETPIGEGTDG-PVYLKDIWPTNEEVQGVINA 600

Query: 600 KVSGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPI 659
            +   MF+  Y  V+ GDAHWQ I      TY W   STYI +PP+F  +++ P P+  I
Sbjct: 601 NIDSEMFKSRYGNVYLGDAHWQKINVEGSATYSWPAASTYIANPPYFAGMTMTPAPVADI 660

Query: 660 KQAYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRG 719
             A  LA+ GDSITTDHISPAGSIKA SPAG +L  + V + DFNSYG+RRGN  VM+RG
Sbjct: 661 VDAKPLAILGDSITTDHISPAGSIKADSPAGKWLMERQVSKADFNSYGARRGNDNVMVRG 720

Query: 720 TFANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRD 779
           TFANIRIRNEM PG EGG+T Y   GETM IYDAAMR++ +   LVI+AGKEYGTGSSRD
Sbjct: 721 TFANIRIRNEMVPGVEGGMTSY--AGETMPIYDAAMRHKADGTPLVIVAGKEYGTGSSRD 778

Query: 780 WAAKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIEISD 839
           WAAKGTNLLGV+AVITESFERIHRSNL+GMG+LPLQF EG TR+TLKLDGSE  +I    
Sbjct: 779 WAAKGTNLLGVRAVITESFERIHRSNLVGMGVLPLQFAEGVTRQTLKLDGSETFTITGVA 838

Query: 840 KLTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKIS 890
            L P   V V + R DG  E   T CRIDT +ELEY+ NGGILQYVLR ++
Sbjct: 839 GLRPRQDVEVKLTRADGSSETFLTRCRIDTVNELEYFLNGGILQYVLRNLA 889


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: 2101
Number of extensions: 88
Number of successful extensions: 8
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: 890
Length adjustment: 43
Effective length of query: 848
Effective length of database: 847
Effective search space:   718256
Effective search space used:   718256
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 Ga0059261_3296 Ga0059261_3296 (aconitate hydratase 1)
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.4805.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 1361.1   0.0          0 1360.9   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3296  Ga0059261_3296 aconitate hydrata


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3296  Ga0059261_3296 aconitate hydratase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1360.9   0.0         0         0       1     875 [.      20     888 ..      20     889 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1360.9 bits;  conditional E-value: 0
                                 TIGR01341   1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkke.elkdeeiafkpar 68 
                                               k++ yysl++++ +l+++s+lp s+++lle++lr  dg +++ ed +a+++w+k+ +  ++ei+++par
  lcl|FitnessBrowser__Korea:Ga0059261_3296  20 KSYSYYSLEKAAAKLGDVSRLPFSMKVLLENMLRFEDGVTVTPEDAQAIVDWQKNpNAPEREIQYRPAR 88 
                                               5789************************************************998345689******** PP

                                 TIGR01341  69 vvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernk 137
                                               v++qdftGvp vvdlaa+r+a+++lg+d++kinp+vpv lvidhsv vd++g+ +a+e+nvele++rn+
  lcl|FitnessBrowser__Korea:Ga0059261_3296  89 VLMQDFTGVPCVVDLAAMRDAITKLGGDAAKINPQVPVHLVIDHSVMVDEFGTPKAFEENVELEYQRNM 157
                                               ********************************************************************* PP

                                 TIGR01341 138 erykflkwakkafknlkvvppgtGivhqvnleylakvvfe.aekdgellaypdslvGtdshttminGlG 205
                                               ery flkw++k++ n+kvvppgtGi+hqvnley+a+++++ +  dg ++aypd+lvGtdshttm+nGlG
  lcl|FitnessBrowser__Korea:Ga0059261_3296 158 ERYDFLKWGSKSLDNFKVVPPGTGICHQVNLEYIADAIWSsTAADGTTVAYPDTLVGTDSHTTMVNGLG 226
                                               **************************************972568************************* PP

                                 TIGR01341 206 vlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeg 274
                                               vlGwGvGGieaeaa+lGqpvs+ +pev+G+kltGkl+eG+tatdlvltvt++lr +gvvg+fveffG+g
  lcl|FitnessBrowser__Korea:Ga0059261_3296 227 VLGWGVGGIEAEAAMLGQPVSMLIPEVVGFKLTGKLQEGITATDLVLTVTQMLRARGVVGRFVEFFGPG 295
                                               ********************************************************************* PP

                                 TIGR01341 275 lkelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepky 342
                                               l++++ladratianmapeyGat++ff idd+tl+y+rltgrd+d+v lve+y+kaq++++  d ++p++
  lcl|FitnessBrowser__Korea:Ga0059261_3296 296 LATMTLADRATIANMAPEYGATCGFFGIDDKTLDYMRLTGRDDDTVTLVEAYCKAQGMWRYdDMADPIF 364
                                               ***********************************************************754999**** PP

                                 TIGR01341 343 tdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeakekklegkeaelkdga 411
                                               td++eld+ +v as+aGpkrpqdrv+l++v++ f+  l +  g+++       ++ ++egk++ + dg+
  lcl|FitnessBrowser__Korea:Ga0059261_3296 365 TDTLELDMATVTASLAGPKRPQDRVSLNKVDEVFNGDLFKVYGKEN------GHRVAVEGKDHDIGDGD 427
                                               ***********************************99988777665......6677889********** PP

                                 TIGR01341 412 vviaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfn 480
                                               vviaaitsctntsnpsvl++agl+a+ka   Gl +kp+vktslapGs+vvtdyl+++gl + l+++Gfn
  lcl|FitnessBrowser__Korea:Ga0059261_3296 428 VVIAAITSCTNTSNPSVLIAAGLVARKARAKGLTRKPWVKTSLAPGSQVVTDYLNKAGLSEDLDAIGFN 496
                                               ********************************************************************* PP

                                 TIGR01341 481 lvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtv 549
                                               lvGyGcttciGnsGpl + +++ai+ nd+++++vlsGnrnfegr+ p+v+an+laspplvvayal Gtv
  lcl|FitnessBrowser__Korea:Ga0059261_3296 497 LVGYGCTTCIGNSGPLAQPISDAINGNDIVAASVLSGNRNFEGRVSPDVRANFLASPPLVVAYALKGTV 565
                                               ********************************************************************* PP

                                 TIGR01341 550 didlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlye 618
                                               + d+ + pig ++dG +vylkdiwp+++e++ +++ ++ +e+fk +y +v  g+++w++++v  s++y+
  lcl|FitnessBrowser__Korea:Ga0059261_3296 566 TEDMIETPIGEGTDG-PVYLKDIWPTNEEVQGVINANIDSEMFKSRYGNVYLGDAHWQKINVEGSATYS 633
                                               **************9.8**************************************************** PP

                                 TIGR01341 619 wdekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverr 687
                                               w   styi +pp+f +++++p+ v di +a+ l+ lGdsittdhispaGsik dspa+k+l+e+ v++ 
  lcl|FitnessBrowser__Korea:Ga0059261_3296 634 WPAASTYIANPPYFAGMTMTPAPVADIVDAKPLAILGDSITTDHISPAGSIKADSPAGKWLMERQVSKA 702
                                               ********************************************************************* PP

                                 TIGR01341 688 dfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGk 756
                                               dfnsyG+rrGn++vm+rGtfaniri+n++v+g eGg+t y   +e++ +ydaam++k +g+plv++aGk
  lcl|FitnessBrowser__Korea:Ga0059261_3296 703 DFNSYGARRGNDNVMVRGTFANIRIRNEMVPGVEGGMTSYA--GETMPIYDAAMRHKADGTPLVIVAGK 769
                                               ****************************************6..689*********************** PP

                                 TIGR01341 757 eyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddie 825
                                               eyG+Gssrdwaakgt+llGv+avi+esferihrsnlvgmGvlpl+f +g +++tl l+g+et  + ++ 
  lcl|FitnessBrowser__Korea:Ga0059261_3296 770 EYGTGSSRDWAAKGTNLLGVRAVITESFERIHRSNLVGMGVLPLQFAEGVTRQTLKLDGSETFTITGVA 838
                                               ********************************************************************* PP

                                 TIGR01341 826 elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkl 875
                                                l+p+++v+v+l+++dg+ et+ +++ridt  el+y+ +gGilqyvlr+l
  lcl|FitnessBrowser__Korea:Ga0059261_3296 839 GLRPRQDVEVKLTRADGSSETFLTRCRIDTVNELEYFLNGGILQYVLRNL 888
                                               ************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (890 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 12.28
//
[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