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.3611297.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 34.40
//
[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