GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Nocardiopsis lucentensis DSM 44048

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_017598314.1 D471_RS0108975 aconitate hydratase AcnA

Query= BRENDA::Q9RIL1
         (931 letters)



>NCBI__GCF_000341125.1:WP_017598314.1
          Length = 904

 Score = 1473 bits (3813), Expect = 0.0
 Identities = 736/931 (79%), Positives = 801/931 (86%), Gaps = 27/931 (2%)

Query: 1   MSANSFDARSTLQVGDESYEIFRLDKVEGSARLPYSLKVLLENLLRTEDGANITADHIRA 60
           MSANSF AR TL+VGDESYEIFRLD V+G+ RLPYSLKVLLENLLRTEDGAN+TADHIRA
Sbjct: 1   MSANSFGARDTLRVGDESYEIFRLDAVQGANRLPYSLKVLLENLLRTEDGANVTADHIRA 60

Query: 61  LGGWDSQAQPSQEIQFTPARVIMQDFTGVPCVVDLATMREAVKELGGDPAKINPLAPAEL 120
           LG WD++AQPSQEIQFTPARVIMQDFTGVPCVVDLATMREAV++LGGDP KINPLAPAEL
Sbjct: 61  LGEWDAKAQPSQEIQFTPARVIMQDFTGVPCVVDLATMREAVRDLGGDPDKINPLAPAEL 120

Query: 121 VIDHSVIADKFGTNDAFKQNVELEYGRNKERYQFLRWGQTAFDEFKVVPPGTGIVHQVNI 180
           VIDHSV+ D FG  DAF++NVE+EY RN ERY+FLRWGQTAFDEFKVVPPGTGIVHQ NI
Sbjct: 121 VIDHSVVVDLFGRPDAFERNVEIEYERNYERYKFLRWGQTAFDEFKVVPPGTGIVHQANI 180

Query: 181 EHLARTVMVRGGQAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSMLIPRV 240
           EHLAR  M R GQAYPDT VGTDSHTTM NGLG+LGWGVGGIEAEAAMLGQP+SMLIPRV
Sbjct: 181 EHLARVTMSRNGQAYPDTCVGTDSHTTMQNGLGILGWGVGGIEAEAAMLGQPISMLIPRV 240

Query: 241 VGFKLTGELKPGTTATDLVLTITEMLRGHGVVGKFVEFYGEGVAATSLANRATIGNMSPE 300
           VGFKL+G+LKPGTTATDLVLTITE LR HGVVGKFVEFYGEGV++  LANRATIGNMSPE
Sbjct: 241 VGFKLSGQLKPGTTATDLVLTITEKLREHGVVGKFVEFYGEGVSSVPLANRATIGNMSPE 300

Query: 301 FGSTAAIFPIDDETLNYLRLTGRSEQQVALVESYAKEQGLWLDPAAEPDFSEKLELDLST 360
           FGSTAAIFP+DDET+ Y+RLTGRSEQQVAL E+YAK  G W DPA EP++SE LELDL+ 
Sbjct: 301 FGSTAAIFPVDDETIRYMRLTGRSEQQVALTEAYAKANGFWHDPAVEPEYSEYLELDLAE 360

Query: 361 VVPSIAGPKRPQDRIVLAEAAQQFAKDVLNYVEAPAAQPAASASPVDEASAESFPASDAP 420
           VVPSIAGPKRPQDRI L+EA   +  DV NYV              DEA  ESFPASDAP
Sbjct: 361 VVPSIAGPKRPQDRIALSEAKPTWRHDVHNYVSD------------DEAGEESFPASDAP 408

Query: 421 AYGSQENGAGARQHADGTGAAVPSNPVTVTAPDGTSYEIDHGAVTVAAITSCTNTSNPYV 480
           A  +  NG              P  PV VT  DGT  E+DHGAV +AAITSCTNTSNP V
Sbjct: 409 A--TTANGR-------------PHRPVKVTMADGTETEVDHGAVVIAAITSCTNTSNPSV 453

Query: 481 MVAAALVAKKAVEKGLTRKPWVKTTLAPGSKVVTDYFEKSGLTPYLDKVGFNLVGYGCTT 540
           M+ AAL+AKKAVEKGL+RKPWVKT++APGSKVVTDY+E+SGLTPYLDK+GFNLVGYGCTT
Sbjct: 454 MLGAALLAKKAVEKGLSRKPWVKTSMAPGSKVVTDYYERSGLTPYLDKLGFNLVGYGCTT 513

Query: 541 CIGNSGPLPEEVSKAVNDHDLAVTSVLSGNRNFEGRINPDVKMNYLASPPLVVAYALAGS 600
           CIGNSGPLPEE+SKAV D+DLAVT+VLSGNRNFEGRINPDVKMNYLASPPLVVAYALAGS
Sbjct: 514 CIGNSGPLPEEISKAVQDNDLAVTAVLSGNRNFEGRINPDVKMNYLASPPLVVAYALAGS 573

Query: 601 MKVDITKDALGTDQDGNPVYLKDIWPSEAEVNDVVANAIGEDMFSKSYSDVFAGDAQWQA 660
           + VDIT + LG   DG PVYL DIWPS  E+ +V+  AI  DM+  +Y+DVFAGD +W++
Sbjct: 574 LDVDITTEPLGVGSDGKPVYLADIWPSAEEIQEVMDAAIASDMYESAYADVFAGDERWRS 633

Query: 661 LPIPTGNTFEWDPESTYVRKPPYFEGMEMEPAPVEDIAGARVLAKLGDSVTTDHISPAGA 720
           LP PTGNTFEW+ ESTYVRKPPYFEGM   P+ V DI GARVLAKLGDSVTTDHISPAGA
Sbjct: 634 LPTPTGNTFEWEDESTYVRKPPYFEGMATTPSAVTDITGARVLAKLGDSVTTDHISPAGA 693

Query: 721 IKADTPAGKYLTEHGVERRDFNSYGSRRGNHEVMIRGTFANIRLRNQIAPGTEGGYTRDF 780
           IK  TPA +YL  HGVERRDFNSYGSRRGNHEVMIRGTFANIRLRNQIAPGTEGGYTRDF
Sbjct: 694 IKPGTPAAEYLKSHGVERRDFNSYGSRRGNHEVMIRGTFANIRLRNQIAPGTEGGYTRDF 753

Query: 781 TKDDAPVSFIYDASRNYIEQGIPLVVLAGKEYGSGSSRDWAAKGTALLGVKAVIAESYER 840
           T+ +APVSFIYDA++NY  Q IPLVVL GKEYGSGSSRDWAAKGT LLGV+AVI ESYER
Sbjct: 754 TQPEAPVSFIYDAAQNYAAQDIPLVVLGGKEYGSGSSRDWAAKGTRLLGVRAVITESYER 813

Query: 841 IHRSNLIGMGVLPLQFPEGQSAATLGLTGEETFSFSGVTELNNGTTPRTVKVTTDTGVEF 900
           IHRSNLIGMGVLPLQFPEGQSA +LGLTGEETFS +GVTELN G  P TVKV+TDTGVEF
Sbjct: 814 IHRSNLIGMGVLPLQFPEGQSADSLGLTGEETFSITGVTELNEGRVPSTVKVSTDTGVEF 873

Query: 901 DAVVRIDTPGEADYYRNGGIMQYVLRSLIRK 931
           DAVVRIDTPGEADYYRNGGI+QYVLR LI K
Sbjct: 874 DAVVRIDTPGEADYYRNGGILQYVLRQLIAK 904


Lambda     K      H
   0.314    0.133    0.386 

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: 2453
Number of extensions: 104
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: 931
Length of database: 904
Length adjustment: 43
Effective length of query: 888
Effective length of database: 861
Effective search space:   764568
Effective search space used:   764568
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: 42 (22.0 bits)
S2: 57 (26.6 bits)

Align candidate WP_017598314.1 D471_RS0108975 (aconitate hydratase AcnA)
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.2626763.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 1316.2   0.0          0 1315.9   0.0    1.0  1  NCBI__GCF_000341125.1:WP_017598314.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000341125.1:WP_017598314.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1315.9   0.0         0         0      15     876 .]      27     902 ..      17     902 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1315.9 bits;  conditional E-value: 0
                             TIGR01341  15 lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdftGvpavvdlaalr 87 
                                            +  ++lp+sl++lle++lr+ dg +++ +++ al +w+++++  +ei+f parv++qdftGvp vvdla++r
  NCBI__GCF_000341125.1:WP_017598314.1  27 VQGANRLPYSLKVLLENLLRTEDGANVTADHIRALGEWDAKAQPSQEIQFTPARVIMQDFTGVPCVVDLATMR 99 
                                           556799******************************************************************* PP

                             TIGR01341  88 eavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkafknlkvvppgt 160
                                           eav++lg+dp+kinpl p++lvidhsv vd +g  +a+e nve+e+ern erykfl+w++ af ++kvvppgt
  NCBI__GCF_000341125.1:WP_017598314.1 100 EAVRDLGGDPDKINPLAPAELVIDHSVVVDLFGRPDAFERNVEIEYERNYERYKFLRWGQTAFDEFKVVPPGT 172
                                           ************************************************************************* PP

                             TIGR01341 161 GivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpvslsvpevi 233
                                           Givhq n+e+la+v ++ +      aypd+ vGtdshttm nGlG+lGwGvGGieaeaa+lGqp+s+ +p v+
  NCBI__GCF_000341125.1:WP_017598314.1 173 GIVHQANIEHLARVTMSRN----GQAYPDTCVGTDSHTTMQNGLGILGWGVGGIEAEAAMLGQPISMLIPRVV 241
                                           **************99988....679*********************************************** PP

                             TIGR01341 234 GvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaffpiddvt 306
                                           G+kl G+l++G+tatdlvlt+te lr++gvvgkfvef+Geg+++++la+rati nm+pe+G+taa+fp+dd+t
  NCBI__GCF_000341125.1:WP_017598314.1 242 GFKLSGQLKPGTTATDLVLTITEKLREHGVVGKFVEFYGEGVSSVPLANRATIGNMSPEFGSTAAIFPVDDET 314
                                           ************************************************************************* PP

                             TIGR01341 307 lqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafkss 379
                                           + y+rltgr+e++v l e+y+ka+++++d + ep+y++ +eldl +v +s+aGpkrpqdr+al+e k ++++ 
  NCBI__GCF_000341125.1:WP_017598314.1 315 IRYMRLTGRSEQQVALTEAYAKANGFWHDPAVEPEYSEYLELDLAEVVPSIAGPKRPQDRIALSEAKPTWRHD 387
                                           **********************************************************************999 PP

                             TIGR01341 380 lesnagekglalr.................keakekklegkeaelkdgavviaaitsctntsnpsvllgagll 435
                                           +++ +++ + + +                 +  k ++ +g+e+e+++gavviaaitsctntsnpsv+lga+ll
  NCBI__GCF_000341125.1:WP_017598314.1 388 VHNYVSDDEAGEEsfpasdapattangrphRPVKVTMADGTETEVDHGAVVIAAITSCTNTSNPSVMLGAALL 460
                                           776665555444444555889999999885444555557********************************** PP

                             TIGR01341 436 akkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikend 508
                                           akkave Gl +kp+vkts+apGskvvtdy  +sgl+pyl++lGfnlvGyGcttciGnsGpl+ee+++a+++nd
  NCBI__GCF_000341125.1:WP_017598314.1 461 AKKAVEKGLSRKPWVKTSMAPGSKVVTDYYERSGLTPYLDKLGFNLVGYGCTTCIGNSGPLPEEISKAVQDND 533
                                           ************************************************************************* PP

                             TIGR01341 509 levsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiae 581
                                           l v+avlsGnrnfegri+p+vk nylaspplvvayalaG++d+d+++ep+g++ dGk+vyl diwpsa+ei+e
  NCBI__GCF_000341125.1:WP_017598314.1 534 LAVTAVLSGNRNFEGRINPDVKMNYLASPPLVVAYALAGSLDVDITTEPLGVGSDGKPVYLADIWPSAEEIQE 606
                                           ************************************************************************* PP

                             TIGR01341 582 lvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillll 654
                                           +++ a+ +++++  y+ v+ g+erw++l +++++++ew+++sty+r+pp+fe++ ++p+ v+di+gar+l++l
  NCBI__GCF_000341125.1:WP_017598314.1 607 VMDAAIASDMYESAYADVFAGDERWRSLPTPTGNTFEWEDESTYVRKPPYFEGMATTPSAVTDITGARVLAKL 679
                                           ************************************************************************* PP

                             TIGR01341 655 GdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvy 727
                                           Gds+ttdhispaG+ik+ +paa+ylk +GverrdfnsyGsrrGnhevm+rGtfanir++n++++g+eGg+t+ 
  NCBI__GCF_000341125.1:WP_017598314.1 680 GDSVTTDHISPAGAIKPGTPAAEYLKSHGVERRDFNSYGSRRGNHEVMIRGTFANIRLRNQIAPGTEGGYTRD 752
                                           ***********************************************************************96 PP

                             TIGR01341 728 l..pdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvl 798
                                           +  p+  v  +ydaa +y  +++plvvl GkeyGsGssrdwaakgt+llGv+avi+es+erihrsnl+gmGvl
  NCBI__GCF_000341125.1:WP_017598314.1 753 FtqPEAPVSFIYDAAQNYAAQDIPLVVLGGKEYGSGSSRDWAAKGTRLLGVRAVITESYERIHRSNLIGMGVL 825
                                           5348888999*************************************************************** PP

                             TIGR01341 799 plefkqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyv 871
                                           pl+f++g++a++lgltgeet  + +++el+ ++  + + v++d     ++av+ridt+ e +y+++gGilqyv
  NCBI__GCF_000341125.1:WP_017598314.1 826 PLQFPEGQSADSLGLTGEETFSITGVTELNEGRVPSTVKVSTD-TGVEFDAVVRIDTPGEADYYRNGGILQYV 897
                                           *****************************98875444334444.45689************************ PP

                             TIGR01341 872 lrkll 876
                                           lr+l+
  NCBI__GCF_000341125.1:WP_017598314.1 898 LRQLI 902
                                           **975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (904 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 31.80
//
[ok]

This GapMind analysis is from Apr 09 2024. 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