Alignments for a candidate for acn in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Escherichia coli BW25113

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 15396 b1276 aconitate hydratase (NCBI)

Query= BRENDA::P25516
         (891 letters)



>FitnessBrowser__Keio:15396
          Length = 891

 Score = 1790 bits (4636), Expect = 0.0
 Identities = 891/891 (100%), Positives = 891/891 (100%)

Query: 1   MSSTLREASKDTLQAKDKTYHYYSLPLAAKSLGDITRLPKSLKVLLENLLRWQDGNSVTE 60
           MSSTLREASKDTLQAKDKTYHYYSLPLAAKSLGDITRLPKSLKVLLENLLRWQDGNSVTE
Sbjct: 1   MSSTLREASKDTLQAKDKTYHYYSLPLAAKSLGDITRLPKSLKVLLENLLRWQDGNSVTE 60

Query: 61  EDIHALAGWLKNAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL 120
           EDIHALAGWLKNAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL
Sbjct: 61  EDIHALAGWLKNAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL 120

Query: 121 SPVDLVIDHSVTVDRFGDDEAFEENVRLEMERNHERYVFLKWGKQAFSRFSVVPPGTGIC 180
           SPVDLVIDHSVTVDRFGDDEAFEENVRLEMERNHERYVFLKWGKQAFSRFSVVPPGTGIC
Sbjct: 121 SPVDLVIDHSVTVDRFGDDEAFEENVRLEMERNHERYVFLKWGKQAFSRFSVVPPGTGIC 180

Query: 181 HQVNLEYLGKAVWSELQDGEWIAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240
           HQVNLEYLGKAVWSELQDGEWIAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ
Sbjct: 181 HQVNLEYLGKAVWSELQDGEWIAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240

Query: 241 PVSMLIPDVVGFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300
           PVSMLIPDVVGFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR
Sbjct: 241 PVSMLIPDVVGFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300

Query: 301 ATIANMSPEYGATCGFFPIDAVTLDYMRLSGRSEDQVELVEKYAKAQGMWRNPGDEPIFT 360
           ATIANMSPEYGATCGFFPIDAVTLDYMRLSGRSEDQVELVEKYAKAQGMWRNPGDEPIFT
Sbjct: 301 ATIANMSPEYGATCGFFPIDAVTLDYMRLSGRSEDQVELVEKYAKAQGMWRNPGDEPIFT 360

Query: 361 STLELDMNDVEASLAGPKRPQDRVALPDVPKAFAASNELEVNATHKDRQPVDYVMNGHQY 420
           STLELDMNDVEASLAGPKRPQDRVALPDVPKAFAASNELEVNATHKDRQPVDYVMNGHQY
Sbjct: 361 STLELDMNDVEASLAGPKRPQDRVALPDVPKAFAASNELEVNATHKDRQPVDYVMNGHQY 420

Query: 421 QLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYL 480
           QLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYL
Sbjct: 421 QLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYL 480

Query: 481 AKAKLTPYLDELGFNLVGYGCTTCIGNSGPLPDPIETAIKKSDLTVGAVLSGNRNFEGRI 540
           AKAKLTPYLDELGFNLVGYGCTTCIGNSGPLPDPIETAIKKSDLTVGAVLSGNRNFEGRI
Sbjct: 481 AKAKLTPYLDELGFNLVGYGCTTCIGNSGPLPDPIETAIKKSDLTVGAVLSGNRNFEGRI 540

Query: 541 HPLVKTNWLASPPLVVAYALAGNMNINLASEPIGHDRKGDPVYLKDIWPSAQEIARAVEQ 600
           HPLVKTNWLASPPLVVAYALAGNMNINLASEPIGHDRKGDPVYLKDIWPSAQEIARAVEQ
Sbjct: 541 HPLVKTNWLASPPLVVAYALAGNMNINLASEPIGHDRKGDPVYLKDIWPSAQEIARAVEQ 600

Query: 601 VSTEMFRKEYAEVFEGTAEWKGINVTRSDTYGWQEDSTYIRLSPFFDEMQATPAPVEDIH 660
           VSTEMFRKEYAEVFEGTAEWKGINVTRSDTYGWQEDSTYIRLSPFFDEMQATPAPVEDIH
Sbjct: 601 VSTEMFRKEYAEVFEGTAEWKGINVTRSDTYGWQEDSTYIRLSPFFDEMQATPAPVEDIH 660

Query: 661 GARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQGRGVERKDFNSYGSRRGNHEVMMRGT 720
           GARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQGRGVERKDFNSYGSRRGNHEVMMRGT
Sbjct: 661 GARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQGRGVERKDFNSYGSRRGNHEVMMRGT 720

Query: 721 FANIRIRNEMVPGVEGGMTRHLPDSDVVSIYDAAMRYKQEQTPLAVIAGKEYGSGSSRDW 780
           FANIRIRNEMVPGVEGGMTRHLPDSDVVSIYDAAMRYKQEQTPLAVIAGKEYGSGSSRDW
Sbjct: 721 FANIRIRNEMVPGVEGGMTRHLPDSDVVSIYDAAMRYKQEQTPLAVIAGKEYGSGSSRDW 780

Query: 781 AAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEKIDIGDLQN 840
           AAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEKIDIGDLQN
Sbjct: 781 AAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEKIDIGDLQN 840

Query: 841 LQPGATVPVTLTRADGSQEVVPCRCRIDTATELTYYQNDGILHYVIRNMLK 891
           LQPGATVPVTLTRADGSQEVVPCRCRIDTATELTYYQNDGILHYVIRNMLK
Sbjct: 841 LQPGATVPVTLTRADGSQEVVPCRCRIDTATELTYYQNDGILHYVIRNMLK 891


Lambda     K      H
   0.317    0.135    0.401 

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: 2572
Number of extensions: 91
Number of successful extensions: 1
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: 891
Length adjustment: 43
Effective length of query: 848
Effective length of database: 848
Effective search space:   719104
Effective search space used:   719104
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 15396 b1276 (aconitate hydratase (NCBI))
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.8135.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 1588.0   0.0          0 1587.8   0.0    1.0  1  lcl|FitnessBrowser__Keio:15396  b1276 aconitate hydratase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15396  b1276 aconitate hydratase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1587.8   0.0         0         0       1     876 []      18     890 ..      18     890 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1587.8 bits;  conditional E-value: 0
                       TIGR01341   1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdftGvpa 79 
                                     k+++yysl+ +++sl++i++lpksl++lle++lr++dg++++eed++al+ w k++++d+eia++parv++qdftGvpa
  lcl|FitnessBrowser__Keio:15396  18 KTYHYYSLPLAAKSLGDITRLPKSLKVLLENLLRWQDGNSVTEEDIHALAGWLKNAHADREIAYRPARVLMQDFTGVPA 96 
                                     689**************************************************************************** PP

                       TIGR01341  80 vvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkafknlkvvpp 158
                                     vvdlaa+reavk+lg+d++k+npl+pvdlvidhsv+vd++g++ea+e+nv+le+ern+ery flkw+k+af++++vvpp
  lcl|FitnessBrowser__Keio:15396  97 VVDLAAMREAVKRLGGDTAKVNPLSPVDLVIDHSVTVDRFGDDEAFEENVRLEMERNHERYVFLKWGKQAFSRFSVVPP 175
                                     ******************************************************************************* PP

                       TIGR01341 159 gtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpvslsvpeviGvkl 237
                                     gtGi+hqvnleyl+k+v+++ +dge++aypd+lvGtdshttminGlGvlGwGvGGieaeaa+lGqpvs+ +p+v+G+kl
  lcl|FitnessBrowser__Keio:15396 176 GTGICHQVNLEYLGKAVWSELQDGEWIAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVGFKL 254
                                     ******************************************************************************* PP

                       TIGR01341 238 tGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaffpiddvtlqylrltgrd 316
                                     tGklreG+tatdlvltvt++lrk+gvvgkfvef+G+gl++l+ladratianm+peyGat++ffpid+vtl+y+rl+gr+
  lcl|FitnessBrowser__Keio:15396 255 TGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEYGATCGFFPIDAVTLDYMRLSGRS 333
                                     ******************************************************************************* PP

                       TIGR01341 317 edkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafkss..lesnagekglalrk 393
                                     ed+velveky+kaq+++++ ++ep++t+++eld++dveas+aGpkrpqdrval +v++af++s  le+na++k+    +
  lcl|FitnessBrowser__Keio:15396 334 EDQVELVEKYAKAQGMWRNPGDEPIFTSTLELDMNDVEASLAGPKRPQDRVALPDVPKAFAASneLEVNATHKD----R 408
                                     ************************************************************9887799******9....* PP

                       TIGR01341 394 eakekklegkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllp 472
                                     ++++++++g++++l dgavviaaitsctntsnpsvl++agllakkav+lGlk++p+vk+slapGskvv+dyla+++l+p
  lcl|FitnessBrowser__Keio:15396 409 QPVDYVMNGHQYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYLAKAKLTP 487
                                     ******************************************************************************* PP

                       TIGR01341 473 yleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdi 551
                                     yl+elGfnlvGyGcttciGnsGpl++ +e+aik++dl+v avlsGnrnfegrihplvk+n+laspplvvayalaG+++i
  lcl|FitnessBrowser__Keio:15396 488 YLDELGFNLVGYGCTTCIGNSGPLPDPIETAIKKSDLTVGAVLSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNI 566
                                     ******************************************************************************* PP

                       TIGR01341 552 dlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyirepp 630
                                     +l++epig+d++G++vylkdiwpsa+eia++  ++v++e+f+key+ev+eg+++w+ ++vt+sd+y w+e+styir++p
  lcl|FitnessBrowser__Keio:15396 567 NLASEPIGHDRKGDPVYLKDIWPSAQEIARA-VEQVSTEMFRKEYAEVFEGTAEWKGINVTRSDTYGWQEDSTYIRLSP 644
                                     ******************************5.578******************************************** PP

                       TIGR01341 631 ffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfan 709
                                     ff+e++++p+ vedi+garil++lGds+ttdhispaGsik+dspa++yl+ +Gver+dfnsyGsrrGnhevm+rGtfan
  lcl|FitnessBrowser__Keio:15396 645 FFDEMQATPAPVEDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQGRGVERKDFNSYGSRRGNHEVMMRGTFAN 723
                                     ******************************************************************************* PP

                       TIGR01341 710 iriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferih 788
                                     iri+n++v+g eGg+t++lpds+vvs+ydaam+yk+e++pl+v+aGkeyGsGssrdwaakg++llG+++viaesferih
  lcl|FitnessBrowser__Keio:15396 724 IRIRNEMVPGVEGGMTRHLPDSDVVSIYDAAMRYKQEQTPLAVIAGKEYGSGSSRDWAAKGPRLLGIRVVIAESFERIH 802
                                     ******************************************************************************* PP

                       TIGR01341 789 rsnlvgmGvlplefkqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveavlridtevelayvkkgGi 867
                                     rsnl+gmG+lplef+qg +++tlgltgee+id+ d+++l+p+++v+v+l+++dg++e+v +++ridt++el+y++++Gi
  lcl|FitnessBrowser__Keio:15396 803 RSNLIGMGILPLEFPQGVTRKTLGLTGEEKIDIGDLQNLQPGATVPVTLTRADGSQEVVPCRCRIDTATELTYYQNDGI 881
                                     ******************************************************************************* PP

                       TIGR01341 868 lqyvlrkll 876
                                     l+yv+r++l
  lcl|FitnessBrowser__Keio:15396 882 LHYVIRNML 890
                                     *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (891 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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 10.71
//
[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