Alignments for a candidate for acn in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Cupriavidus basilensis 4G11

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate RR42_RS14490 RR42_RS14490 aconitate hydratase

Query= BRENDA::A0A090AMG4
         (901 letters)



>FitnessBrowser__Cup4G11:RR42_RS14490
          Length = 901

 Score = 1458 bits (3775), Expect = 0.0
 Identities = 731/904 (80%), Positives = 803/904 (88%), Gaps = 6/904 (0%)

Query: 1   MPHNTLDTLKNFKIGNKSC-QYYSLPALGKSLGIDVQRLPVSIRIVLESVLRNCDGKKVT 59
           MPHN   TLK FKIG  S  Q+YSLP LGK+LG+ V+RLPVSIR+VLESVLRNCDGKKVT
Sbjct: 1   MPHNLNKTLKEFKIGPSSKGQFYSLPQLGKALGVAVERLPVSIRVVLESVLRNCDGKKVT 60

Query: 60  EEHVKQLANWQANARREDEIPFVVARVVLQDFTGVPLLADIAAMRSVADKMGKSPKSIEP 119
           EEHV+QLA+W+  A R DEIPFVVARVVLQDFTGVPLLAD+AAMR+VA+KMGK+PK IEP
Sbjct: 61  EEHVRQLAHWKPVAERVDEIPFVVARVVLQDFTGVPLLADLAAMRNVAEKMGKNPKKIEP 120

Query: 120 LVPVDLVVDHSVMIDYFGTKNALDLNMKLEFKRNQERYQFMKWGMQAFDTFGVVPPGFGI 179
           LVPVDLVVDHSV ID+F  KNALDLNMKLEF+RN ERYQFMKWGMQAFDTFGVV PGFGI
Sbjct: 121 LVPVDLVVDHSVQIDHFREKNALDLNMKLEFQRNNERYQFMKWGMQAFDTFGVVQPGFGI 180

Query: 180 VHQVNLEYLARGVHLDKKNNVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQP 239
           VHQVNLEYLARGVH  KK+ VYYPD+LVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQP
Sbjct: 181 VHQVNLEYLARGVH--KKDGVYYPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQP 238

Query: 240 VYFLTPDVVGVELKGQLRGGVTATDLVLTITEMLRREKVVGKFVEFCGEGTASLSVAERA 299
           VYFLTPDVVGVELKG+LR GVTATDLVLTITEMLRREKVVGKFVEF GEGTASL++ +RA
Sbjct: 239 VYFLTPDVVGVELKGRLREGVTATDLVLTITEMLRREKVVGKFVEFFGEGTASLALPDRA 298

Query: 300 TIGNMAPEYGATMGFFPVDERTIDYFRGTGRTEAEIAAFEAYFKAQKMFGVPKAADINFT 359
           TIGNMAPEYGATMGFFPVDE+TIDYF+GTGRTE EIAAFE YF+AQKMFGVPKA +I++T
Sbjct: 299 TIGNMAPEYGATMGFFPVDEKTIDYFKGTGRTEEEIAAFEGYFRAQKMFGVPKAGEIDYT 358

Query: 360 KLLTLDLSTVAPSLAGPKRPQDRIEIGNVKNTFIDLYSKPVAENGFNQPAEKLAQTFTTS 419
            ++TLDL TVAPSLAGPKRPQDRIEIGNVK+TF  L++KP AENGFN+   +L +T+TT+
Sbjct: 359 NVVTLDLGTVAPSLAGPKRPQDRIEIGNVKSTFASLFAKPTAENGFNKDIAELDKTYTTA 418

Query: 420 AGTQVKNGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVPKHIKTSLAPGSRVVT 479
            G  VK+GD+LIAAITSCTNTSNPSVLLAAGLLAKKAVEAGL V  HIKTSLAPGSRVVT
Sbjct: 419 DGVNVKSGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVAPHIKTSLAPGSRVVT 478

Query: 480 EYLTKTGLLPYLEKLGFDVAAYGCTTCIGNAGDLTPDLNEAIIGNDLICSAVLSGNRNFE 539
           EYL   GLLPYLEKLGF V AYGCTTCIGNAGDLTP+LNEAI  NDL+ +AVLSGNRNFE
Sbjct: 479 EYLQAAGLLPYLEKLGFGVTAYGCTTCIGNAGDLTPELNEAITRNDLVAAAVLSGNRNFE 538

Query: 540 ARIHPNIKANFLASPPLVVAYALAGTVTRDLMTEPVGRGKNG-DVWLGDIWPTTEEIESL 598
           ARIHPNI+ANFLASPPLVVAYA+AG VTRDLMTEPVG GK G +++LGDIWPT+EEI +L
Sbjct: 539 ARIHPNIRANFLASPPLVVAYAIAGNVTRDLMTEPVGTGKGGREIYLGDIWPTSEEIHAL 598

Query: 599 LKYALDPKAFEANYGQVKSNPGKLWENTKGVTGDTYNWPDSTYIAEPPFFEGFGMTPGA- 657
           +KYA+D K F+ NY QVK  P KLW   KG  G  Y+WP STYIAEPPFF+GFGM P A 
Sbjct: 599 MKYAMDSKVFKINYEQVK-KPSKLWAKVKGTKGQVYDWPKSTYIAEPPFFDGFGMEPAAT 657

Query: 658 MPAVKGARALGVFGDSVTTDHISPAGSIKETSPAGKWLKENGVMKADFNSYGSRRGNHEI 717
             +V+ ARALGVFGDSVTTDHISPAGSIKE+SPAGK+L  NGV+KADFNSYGSRRGNHE+
Sbjct: 658 QSSVRNARALGVFGDSVTTDHISPAGSIKESSPAGKYLLANGVLKADFNSYGSRRGNHEV 717

Query: 718 MMRGTFANVRIKNLMIPALPDGSRFEGGETLFQPTGEQMSIYDAAMKYVSAGTPTVVFGG 777
           MMRGTFANVRIKNLM+P   DGSR EGG TL QP+GE +SIYDAAMKY++ GTPTVVFGG
Sbjct: 718 MMRGTFANVRIKNLMLPVKADGSRVEGGVTLHQPSGEALSIYDAAMKYIAEGTPTVVFGG 777

Query: 778 EEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGADSVQSLGITG 837
           EEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKG+DSVQ+LGI G
Sbjct: 778 EEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGSDSVQTLGIVG 837

Query: 838 EETYDISGLEDGIKPMQDVTLTITRKDGSKQDVTVLLRIDTPIEVDYYQHGGILPFVLRQ 897
           +ET+DI G+E  +KP QDVTL I R +G  Q V +LLRIDTPIEVDYY HGGILPFVLRQ
Sbjct: 838 DETFDIEGIEGELKPQQDVTLVIKRANGDVQRVPLLLRIDTPIEVDYYNHGGILPFVLRQ 897

Query: 898 LLAA 901
           LLAA
Sbjct: 898 LLAA 901


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: 2428
Number of extensions: 90
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: 901
Length adjustment: 43
Effective length of query: 858
Effective length of database: 858
Effective search space:   736164
Effective search space used:   736164
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 RR42_RS14490 RR42_RS14490 (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.14853.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 1300.0   0.0          0 1299.8   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS14490  RR42_RS14490 aconitate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS14490  RR42_RS14490 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1299.8   0.0         0         0       3     876 .]      20     899 ..      18     899 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1299.8 bits;  conditional E-value: 0
                                 TIGR01341   3 vyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvv 70 
                                                ++ysl++l ++ +  +++lp s+r++lesvlrn+dg+k++ee+v +l++wk  + +  ei+f +arvv
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490  20 GQFYSLPQLGKAlGVAVERLPVSIRVVLESVLRNCDGKKVTEEHVRQLAHWKPVAERVDEIPFVVARVV 88 
                                               689******9987889***************************************************** PP

                                 TIGR01341  71 lqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernker 139
                                               lqdftGvp++ dlaa+r+  +++gk+p+ki+plvpvdlv+dhsvq+d+++e++al+ n++lef+rn+er
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490  89 LQDFTGVPLLADLAAMRNVAEKMGKNPKKIEPLVPVDLVVDHSVQIDHFREKNALDLNMKLEFQRNNER 157
                                               ********************************************************************* PP

                                 TIGR01341 140 ykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlG 208
                                               y+f+kw+ +af  + vv pg Givhqvnleyla+ v++++     + ypd+lvGtdshttminG+Gv+G
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490 158 YQFMKWGMQAFDTFGVVQPGFGIVHQVNLEYLARGVHKKD----GVYYPDTLVGTDSHTTMINGIGVVG 222
                                               ************************************9987....789********************** PP

                                 TIGR01341 209 wGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglke 277
                                               wGvGGieaea++lGqpv++  p+v+Gv l+G+lreGvtatdlvlt+te+lr++ vvgkfveffGeg ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490 223 WGVGGIEAEAGMLGQPVYFLTPDVVGVELKGRLREGVTATDLVLTITEMLRREKVVGKFVEFFGEGTAS 291
                                               ********************************************************************* PP

                                 TIGR01341 278 lsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdv 345
                                               l+l+drati nmapeyGat++ffp+d++t++y++ tgr e+++   e y +aq++f   ++ e+ yt+v
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490 292 LALPDRATIGNMAPEYGATMGFFPVDEKTIDYFKGTGRTEEEIAAFEGYFRAQKMFGVpKAGEIDYTNV 360
                                               ********************************************************98899******** PP

                                 TIGR01341 346 veldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeakekkl.egkeaelkdgavv 413
                                               v ldl +v +s+aGpkrpqdr+++ +vk++f+s + ++++e+g++ +    +k+    +  ++k+g+v 
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490 361 VTLDLGTVAPSLAGPKRPQDRIEIGNVKSTFASLFAKPTAENGFNKDIAELDKTYtTADGVNVKSGDVL 429
                                               ******************************************9988755555544057899******** PP

                                 TIGR01341 414 iaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlv 482
                                               iaaitsctntsnpsvll+agllakkave+Glkv p++ktslapGs+vvt+yl+ +gllpyle+lGf + 
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490 430 IAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVAPHIKTSLAPGSRVVTEYLQAAGLLPYLEKLGFGVT 498
                                               ********************************************************************* PP

                                 TIGR01341 483 GyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdi 551
                                                yGcttciGn+G+l+ e++eai+ ndl+++avlsGnrnfe+rihp ++an+laspplvvaya+aG+v+ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490 499 AYGCTTCIGNAGDLTPELNEAITRNDLVAAAVLSGNRNFEARIHPNIRANFLASPPLVVAYAIAGNVTR 567
                                               ********************************************************************* PP

                                 TIGR01341 552 dlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewd 620
                                               dl +ep+gt+k G+++yl diwp+ +ei++l+k a+ +++fk +ye+v++ ++ w +++ t++++y+w 
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490 568 DLMTEPVGTGKGGREIYLGDIWPTSEEIHALMKYAMDSKVFKINYEQVKKPSKLWAKVKGTKGQVYDW- 635
                                               ********************************************************************. PP

                                 TIGR01341 621 ekstyireppffeelklepeeved.ikgarillllGdsittdhispaGsikkdspaakylkekGverrd 688
                                               +kstyi eppff+++ +ep+  ++ +++ar l ++Gds+ttdhispaGsik+ spa+kyl  +Gv + d
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490 636 PKSTYIAEPPFFDGFGMEPAATQSsVRNARALGVFGDSVTTDHISPAGSIKESSPAGKYLLANGVLKAD 704
                                               79*****************988766******************************************** PP

                                 TIGR01341 689 fnsyGsrrGnhevmlrGtfaniriknklvkgk......eGgltvylpdsevvsvydaamkykkegvplv 751
                                               fnsyGsrrGnhevm+rGtfan+rikn +++ k      eGg+t++ p +e +s+ydaamky  eg+p+v
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490 705 FNSYGSRRGNHEVMMRGTFANVRIKNLMLPVKadgsrvEGGVTLHQPSGEALSIYDAAMKYIAEGTPTV 773
                                               ****************************87432233349****************************** PP

                                 TIGR01341 752 vlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetid 820
                                               v  G+eyG+Gssrdwaakgt+llGvkavi++sferihrsnlvgmGvlpl+fk  ++ +tlg+ g+et d
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490 774 VFGGEEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGSDSVQTLGIVGDETFD 842
                                               ********************************************************************* PP

                                 TIGR01341 821 vddie.elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
                                               +++ie elkp+++vt+++ +++g+++ v   lridt++e++y+++gGil +vlr+ll
  lcl|FitnessBrowser__Cup4G11:RR42_RS14490 843 IEGIEgELKPQQDVTLVIKRANGDVQRVPLLLRIDTPIEVDYYNHGGILPFVLRQLL 899
                                               ***9659***********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (901 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 0.01s 00:00:00.06 Elapsed: 00:00:00.07
# Mc/sec: 10.09
//
[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:

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 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