Alignments for a candidate for acn in Amantichitinum ursilacus IGB-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Amantichitinum ursilacus IGB-41

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_053935982.1 WG78_RS01355 aconitate hydratase AcnA

Query= BRENDA::A0A090AMG4
         (901 letters)



>NCBI__GCF_001294205.1:WP_053935982.1
          Length = 897

 Score = 1244 bits (3219), Expect = 0.0
 Identities = 624/902 (69%), Positives = 735/902 (81%), Gaps = 9/902 (0%)

Query: 1   MPHNTLDTLKNFKIGNKSCQYYSLPALGKSLGID-VQRLPVSIRIVLESVLRNCDGKKVT 59
           MPH   +TLK       + QYYSLPAL ++ GI  + RLPVSIR+VLESVLRNCDGKKVT
Sbjct: 1   MPHALHNTLKTLPDTAPALQYYSLPAL-EAAGIGPISRLPVSIRLVLESVLRNCDGKKVT 59

Query: 60  EEHVKQLANWQANARREDEIPFVVARVVLQDFTGVPLLADIAAMRSVADKMGKSPKSIEP 119
           EEHV+QLANW+    R DEIPFVVARVVLQDFTGVPLLAD+AAMR+VADK+GK+PK IEP
Sbjct: 60  EEHVRQLANWKPTGHRVDEIPFVVARVVLQDFTGVPLLADLAAMRNVADKLGKNPKLIEP 119

Query: 120 LVPVDLVVDHSVMIDYFGTKNALDLNMKLEFKRNQERYQFMKWGMQAFDTFGVVPPGFGI 179
           LVPVDLVVDHSV +DY+GT +AL  NM++EF+RN ERYQFMKWGMQAFDTF VVPPG GI
Sbjct: 120 LVPVDLVVDHSVQVDYYGTPDALRKNMEMEFQRNSERYQFMKWGMQAFDTFKVVPPGVGI 179

Query: 180 VHQVNLEYLARGVHLDKKNNVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQP 239
           VHQVNLEYL RGV +  ++ + +PD+LVGTDSHTTMIN +GVVGWGVGGIEAEAGMLGQP
Sbjct: 180 VHQVNLEYLFRGVQV--RDGIAFPDTLVGTDSHTTMINAVGVVGWGVGGIEAEAGMLGQP 237

Query: 240 VYFLTPDVVGVELKGQLRGGVTATDLVLTITEMLRREKVVGKFVEFCGEGTASLSVAERA 299
           VYFLTPDV+GVEL G LR GVTATDLVL +TE+LR EKVVGKFVEF G GTASL+V +RA
Sbjct: 238 VYFLTPDVIGVELSGHLREGVTATDLVLAVTELLRHEKVVGKFVEFFGPGTASLTVTDRA 297

Query: 300 TIGNMAPEYGATMGFFPVDERTIDYFRGTGRTEAEIAAFEAYFKAQKMFGVPKAADINFT 359
           TI NMAPEYGATMGFFPVDE+TI Y +GTGRT+AEIA FEAYFKAQ +FG+P+A +I++T
Sbjct: 298 TIANMAPEYGATMGFFPVDEKTIAYLQGTGRTDAEIAQFEAYFKAQNLFGIPQAGEIDYT 357

Query: 360 KLLTLDLSTVAPSLAGPKRPQDRIEIGNVKNTFIDLYSKPVAENGFNQPAEKLAQTFTTS 419
           +++ LDL  + PSLAGPKRPQDRI +  +K +F  L++ PV  NGFN+ + +LA+ + T+
Sbjct: 358 RVVKLDLDGIVPSLAGPKRPQDRIALTAMKTSFNSLFAAPVTANGFNKKSSQLAERYPTA 417

Query: 420 -AGTQVKNGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVPKHIKTSLAPGSRVV 478
             G  + NGDILIAAITSCTNTSNP V+LA+GLLAKKAVE GL+V  HIKTSLAPGSRVV
Sbjct: 418 RQGIDIGNGDILIAAITSCTNTSNPGVMLASGLLAKKAVEKGLSVKPHIKTSLAPGSRVV 477

Query: 479 TEYLTKTGLLPYLEKLGFDVAAYGCTTCIGNAGDLTPDLNEAIIGNDLICSAVLSGNRNF 538
           TEYLT+TGLL  L +LGF +A YGCTTCIGNAGDL P+ NEAI  +D++ +AVLSGNRNF
Sbjct: 478 TEYLTRTGLLEPLAQLGFALAGYGCTTCIGNAGDLAPEFNEAIQLHDVVAAAVLSGNRNF 537

Query: 539 EARIHPNIKANFLASPPLVVAYALAGTVTRDLMTEPVGRGKNGD-VWLGDIWPTTEEIES 597
           EARIHPNI+ANFLASPPLVVA+A+AG    DL TEP+G GK+G  V+L DIWP+++E+  
Sbjct: 538 EARIHPNIRANFLASPPLVVAFAIAGRANIDLTTEPLGTGKDGQPVYLRDIWPSSDEVAE 597

Query: 598 LLKYALDPKAFEANYGQVKSNPGKLWENTKGVTGDTYNWPDSTYIAEPPFFEGFGMTPGA 657
           LLK+ALDP+ F   Y  +  +   LW N     G  Y+WP+STYIA PPFF+ F  TPG+
Sbjct: 598 LLKFALDPEVFRTLYSDLTKDL-DLWNNIPAPQGQVYSWPESTYIARPPFFDQFSPTPGS 656

Query: 658 MPAVKGARALGVFGDSVTTDHISPAGSIKETSPAGKWLKENGVMKADFNSYGSRRGNHEI 717
           +  +KGARAL V GDSVTTDHISPAGS  E +PAG++L  +GV + DFNSYGSRRGNH++
Sbjct: 657 IDDIKGARALLVLGDSVTTDHISPAGSFGEKTPAGQYLIAHGVARPDFNSYGSRRGNHDV 716

Query: 718 MMRGTFANVRIKNLMIPALPDGSRFEGGETLFQPTGEQMSIYDAAMKYVSAGTPTVVFGG 777
           M+RGTFANVR+KNLM+PA  DG R EGG TL   T    ++YDAA  Y+  G PT+VF G
Sbjct: 717 MIRGTFANVRVKNLMLPAKADGGRVEGGFTLLDNT--LSTVYDAAQAYMERGAPTIVFAG 774

Query: 778 EEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGADSVQSLGITG 837
           EEYGTGSSRDWAAKGT LLGVKAVI +SFERIHRSNLVGMGVLPLQFKG DSVQSLGITG
Sbjct: 775 EEYGTGSSRDWAAKGTLLLGVKAVIAKSFERIHRSNLVGMGVLPLQFKGNDSVQSLGITG 834

Query: 838 EETYDISGLEDGIKPMQDVTLTITRKDGSKQDVTVLLRIDTPIEVDYYQHGGILPFVLRQ 897
            E + + G+++ +KP QD+TL I   DG KQ + VL RIDTPIEVDYY+HGGILP+VLR 
Sbjct: 835 NELFAVLGVDEHLKPQQDLTLVICHPDGQKQHIPVLCRIDTPIEVDYYKHGGILPYVLRD 894

Query: 898 LL 899
           LL
Sbjct: 895 LL 896


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: 2279
Number of extensions: 88
Number of successful extensions: 6
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: 901
Length of database: 897
Length adjustment: 43
Effective length of query: 858
Effective length of database: 854
Effective search space:   732732
Effective search space used:   732732
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 WP_053935982.1 WG78_RS01355 (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.2250644.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 1268.1   0.0          0 1267.9   0.0    1.0  1  NCBI__GCF_001294205.1:WP_053935982.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001294205.1:WP_053935982.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1267.9   0.0         0         0       3     876 .]      19     896 ..      17     896 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1267.9 bits;  conditional E-value: 0
                             TIGR01341   3 vyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdf 74 
                                            +yysl+ale + ++ is+lp s+r++lesvlrn+dg+k++ee+v +l++wk + ++  ei+f +arvvlqdf
  NCBI__GCF_001294205.1:WP_053935982.1  19 LQYYSLPALEAAgIGPISRLPVSIRLVLESVLRNCDGKKVTEEHVRQLANWKPTGHRVDEIPFVVARVVLQDF 91 
                                           58********887899********************************************************* PP

                             TIGR01341  75 tGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwak 147
                                           tGvp++ dlaa+r+   +lgk+p++i+plvpvdlv+dhsvqvd++g+ +al++n+e+ef+rn ery+f+kw+ 
  NCBI__GCF_001294205.1:WP_053935982.1  92 TGVPLLADLAAMRNVADKLGKNPKLIEPLVPVDLVVDHSVQVDYYGTPDALRKNMEMEFQRNSERYQFMKWGM 164
                                           ************************************************************************* PP

                             TIGR01341 148 kafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaal 220
                                           +af  +kvvppg Givhqvnleyl + v   +     +a+pd+lvGtdshttmin +Gv+GwGvGGieaea++
  NCBI__GCF_001294205.1:WP_053935982.1 165 QAFDTFKVVPPGVGIVHQVNLEYLFRGVQVRD----GIAFPDTLVGTDSHTTMINAVGVVGWGVGGIEAEAGM 233
                                           *************************9998766....79*********************************** PP

                             TIGR01341 221 lGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapey 293
                                           lGqpv++  p+viGv l G+lreGvtatdlvl vtellr++ vvgkfveffG+g ++l+++dratianmapey
  NCBI__GCF_001294205.1:WP_053935982.1 234 LGQPVYFLTPDVIGVELSGHLREGVTATDLVLAVTELLRHEKVVGKFVEFFGPGTASLTVTDRATIANMAPEY 306
                                           ************************************************************************* PP

                             TIGR01341 294 Gataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkrpqd 365
                                           Gat++ffp+d++t+ yl+ tgr + ++   e+y kaq+lf   ++ e+ yt+vv+ldl+ + +s+aGpkrpqd
  NCBI__GCF_001294205.1:WP_053935982.1 307 GATMGFFPVDEKTIAYLQGTGRTDAEIAQFEAYFKAQNLFGIpQAGEIDYTRVVKLDLDGIVPSLAGPKRPQD 379
                                           ****************************************98899**************************** PP

                             TIGR01341 366 rvalkevkaafksslesnagekglalr..keakekklegkeaelkdgavviaaitsctntsnpsvllgaglla 436
                                           r+al+++k++f+s +  +++ +g++ +  + a+++    +   + +g++ iaaitsctntsnp v+l++glla
  NCBI__GCF_001294205.1:WP_053935982.1 380 RIALTAMKTSFNSLFAAPVTANGFNKKssQLAERYPTARQGIDIGNGDILIAAITSCTNTSNPGVMLASGLLA 452
                                           ***********************9877434555666679999******************************* PP

                             TIGR01341 437 kkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendl 509
                                           kkave Gl vkp++ktslapGs+vvt+yl+++gll+ l +lGf l GyGcttciGn+G+l  e +eai+  d+
  NCBI__GCF_001294205.1:WP_053935982.1 453 KKAVEKGLSVKPHIKTSLAPGSRVVTEYLTRTGLLEPLAQLGFALAGYGCTTCIGNAGDLAPEFNEAIQLHDV 525
                                           ************************************************************************* PP

                             TIGR01341 510 evsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiael 582
                                           +++avlsGnrnfe+rihp ++an+laspplvva+a+aG+ +idl++ep+gt+kdG++vyl+diwps +e+ael
  NCBI__GCF_001294205.1:WP_053935982.1 526 VAAAVLSGNRNFEARIHPNIRANFLASPPLVVAFAIAGRANIDLTTEPLGTGKDGQPVYLRDIWPSSDEVAEL 598
                                           ************************************************************************* PP

                             TIGR01341 583 vkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllG 655
                                            k a+ +e+f+  y+ +t++ + wn++ ++++++y+w ++styi +ppff++++ +p +++dikgar ll+lG
  NCBI__GCF_001294205.1:WP_053935982.1 599 LKFALDPEVFRTLYSDLTKDLDLWNNIPAPQGQVYSW-PESTYIARPPFFDQFSPTPGSIDDIKGARALLVLG 670
                                           *************************************.67********************************* PP

                             TIGR01341 656 dsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgk......eG 722
                                           ds+ttdhispaGs  + +pa++yl+ +Gv r dfnsyGsrrGnh+vm+rGtfan+r+kn ++++k      eG
  NCBI__GCF_001294205.1:WP_053935982.1 671 DSVTTDHISPAGSFGEKTPAGQYLIAHGVARPDFNSYGSRRGNHDVMIRGTFANVRVKNLMLPAKadggrvEG 743
                                           *************************************************************997622222245 PP

                             TIGR01341 723 gltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgm 795
                                           g+t  l d+   +vydaa  y + g p++v aG+eyG+Gssrdwaakgt llGvkavia+sferihrsnlvgm
  NCBI__GCF_001294205.1:WP_053935982.1 744 GFT--LLDNTLSTVYDAAQAYMERGAPTIVFAGEEYGTGSSRDWAAKGTLLLGVKAVIAKSFERIHRSNLVGM 814
                                           555..56899999************************************************************ PP

                             TIGR01341 796 Gvlplefkqgedaetlgltgeetidvddi.eelkpkkevtvelvkedgeketveavlridtevelayvkkgGi 867
                                           Gvlpl+fk  ++ ++lg+tg+e   v ++ e+lkp++++t+++ + dg+k+ + + +ridt++e++y+k+gGi
  NCBI__GCF_001294205.1:WP_053935982.1 815 GVLPLQFKGNDSVQSLGITGNELFAVLGVdEHLKPQQDLTLVICHPDGQKQHIPVLCRIDTPIEVDYYKHGGI 887
                                           **********************8888776267***************************************** PP

                             TIGR01341 868 lqyvlrkll 876
                                           l yvlr+ll
  NCBI__GCF_001294205.1:WP_053935982.1 888 LPYVLRDLL 896
                                           ******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (897 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 39.54
//
[ok]

This GapMind analysis is from Sep 24 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources