GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Pseudomonas fluorescens FW300-N2C3

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate AO356_02385 AO356_02385 aconitate hydratase

Query= reanno::Marino:GFF3491
         (919 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 AO356_02385
           aconitate hydratase
          Length = 913

 Score = 1311 bits (3394), Expect = 0.0
 Identities = 649/912 (71%), Positives = 744/912 (81%), Gaps = 5/912 (0%)

Query: 7   SKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSH 66
           S DSL TL +L    +T+HY+SLP AA +LGDL++LP SLKVL+ENLLR ED  TV  + 
Sbjct: 3   SLDSLKTLKTLQVDARTYHYFSLPDAARSLGDLDKLPMSLKVLLENLLRWEDEKTVTGAD 62

Query: 67  IDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSP 126
           + A+  W+K+R SD EIQ+RPARVLMQDFTGVP VVDLAAMR AV+ AG DP  INPLSP
Sbjct: 63  LKALAGWLKERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAVEKAGGDPQRINPLSP 122

Query: 127 VDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQ 186
           VDLVIDHSVMVDKF  + +F+ NV IEM+RN ERY FLRWGQ AFDNF VVPPGTGICHQ
Sbjct: 123 VDLVIDHSVMVDKFASSQAFEQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQ 182

Query: 187 VNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPV 246
           VNLEYLG+TVW K++DG+T A+PDTLVGTDSHTTMINGLG+LGWGVGGIEAEAAMLGQPV
Sbjct: 183 VNLEYLGRTVWTKEEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 242

Query: 247 SMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRAT 306
           SMLIPEV+GFK+ GKLREGITATDLVLTVT+MLRKKGVVGKFVEFYGDGL D+P+ADRAT
Sbjct: 243 SMLIPEVIGFKLIGKLREGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRAT 302

Query: 307 IANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDN 366
           IANMAPEYGATCGFFPVDE T+ Y+RL+GR  E ++LVEAY KAQGLWR PG EPV+TD 
Sbjct: 303 IANMAPEYGATCGFFPVDEVTLDYLRLSGRPAETVKLVEAYCKAQGLWRLPGQEPVFTDT 362

Query: 367 LELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGGQ-TAVG 425
           LELDMG VEASLAGPKRPQDRV+L N+  +F   +     P    E  LESEGG   AVG
Sbjct: 363 LELDMGSVEASLAGPKRPQDRVSLPNVGQAFSDFLGLQVKPTSKEEGRLESEGGGGVAVG 422

Query: 426 VDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQKGLS 485
             D          E  G   RL  GAVVIAAITSCTNTSNPSVMMAAGL+A+KAV+KGL 
Sbjct: 423 NADQV---GEAEYEFEGHTHRLKNGAVVIAAITSCTNTSNPSVMMAAGLLAKKAVEKGLV 479

Query: 486 TKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEKAIS 545
            KPWVK+SLAPGSKVVTDY    G  + LDKLGF+LVGYGCTTCIGNSGPLPD +EKAI 
Sbjct: 480 RKPWVKSSLAPGSKVVTDYYNAAGLTEYLDKLGFDLVGYGCTTCIGNSGPLPDPIEKAIQ 539

Query: 546 DGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDKDGN 605
             DLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAG VR+D+S +PLGND+DG 
Sbjct: 540 KADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDRDGK 599

Query: 606 PVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKSTYI 665
           PVYL+D+WPS QE+A AV +V T MF KEYA VF GD  W++I+VP++  Y W D STYI
Sbjct: 600 PVYLRDIWPSSQEVAAAVAQVNTSMFHKEYAAVFAGDEQWQAIEVPQAATYVWQDDSTYI 659

Query: 666 QHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHGVEP 725
           QHPPFF+ +   P A+ +++ A +LALLGDSVTTDHISPAG+ K D+PAG+YL+E GVEP
Sbjct: 660 QHPPFFDDIGGPPPAVRNVEGARVLALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEP 719

Query: 726 KDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKYQEK 785
           +DFNSYGSRRGNH+VMMRGTFAN+RIRNEMLDG EGG T ++P+GE+M IYDAAM YQ  
Sbjct: 720 RDFNSYGSRRGNHQVMMRGTFANIRIRNEMLDGEEGGNTIYIPSGERMPIYDAAMLYQAT 779

Query: 786 GTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFPEGT 845
            TPLVVIAG+EYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+PLQF    
Sbjct: 780 DTPLVVIAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQ 839

Query: 846 DRKSLKLTGEETISIEGLSG-EIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYFKH 904
           +RKSL LTG ET+ I GL+  E+ P   L + +  +DG  E  E+  RIDT NE  YFK 
Sbjct: 840 NRKSLNLTGRETLDILGLNDVELTPRMNLPLVITREDGRQERIEVLCRIDTLNEVEYFKA 899

Query: 905 GGILHYVVREML 916
           GGILHYV+R+++
Sbjct: 900 GGILHYVLRQLI 911


Lambda     K      H
   0.315    0.134    0.390 

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: 2321
Number of extensions: 101
Number of successful extensions: 3
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: 919
Length of database: 913
Length adjustment: 43
Effective length of query: 876
Effective length of database: 870
Effective search space:   762120
Effective search space used:   762120
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 AO356_02385 AO356_02385 (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.3252.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 1422.2   0.0          0 1422.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385  AO356_02385 aconitate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385  AO356_02385 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1422.0   0.0         0         0       2     876 .]      19     911 ..      18     911 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1422.0 bits;  conditional E-value: 0
                                       TIGR01341   2 kvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiaf 64 
                                                     +++y+sl+ ++ sl++++klp sl++lle++lr+ d+++++  d++al+ w ke  +d+ei++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385  19 TYHYFSLPDAARSLGDLDKLPMSLKVLLENLLRWEDEKTVTGADLKALAGWLKERRSDREIQY 81 
                                                     79************************************************************* PP

                                       TIGR01341  65 kparvvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealea 127
                                                     +parv++qdftGvpavvdlaa+r av++ g+dp++inpl+pvdlvidhsv vdk+ +++a+e+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385  82 RPARVLMQDFTGVPAVVDLAAMRAAVEKAGGDPQRINPLSPVDLVIDHSVMVDKFASSQAFEQ 144
                                                     *************************************************************** PP

                                       TIGR01341 128 nvelefernkerykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypds 190
                                                     nv++e++rn ery+fl+w++ af n++vvppgtGi+hqvnleyl++ v+++e+dg+++a+pd+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 145 NVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQVNLEYLGRTVWTKEEDGRTYAFPDT 207
                                                     *************************************************************** PP

                                       TIGR01341 191 lvGtdshttminGlGvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvlt 253
                                                     lvGtdshttminGlGvlGwGvGGieaeaa+lGqpvs+ +peviG+kl GklreG+tatdlvlt
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 208 LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLIGKLREGITATDLVLT 270
                                                     *************************************************************** PP

                                       TIGR01341 254 vtellrkkgvvgkfveffGeglkelsladratianmapeyGataaffpiddvtlqylrltgrd 316
                                                     vt++lrkkgvvgkfvef+G+gl+ l+ladratianmapeyGat++ffp+d+vtl+ylrl+gr+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 271 VTQMLRKKGVVGKFVEFYGDGLADLPLADRATIANMAPEYGATCGFFPVDEVTLDYLRLSGRP 333
                                                     *************************************************************** PP

                                       TIGR01341 317 edkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafkss 379
                                                      ++v+lve+y+kaq+l++  ++ep++td++eld+ +veas+aGpkrpqdrv+l +v +af   
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 334 AETVKLVEAYCKAQGLWRLPGQEPVFTDTLELDMGSVEASLAGPKRPQDRVSLPNVGQAFSDF 396
                                                     ************************************************************998 PP

                                       TIGR01341 380 ..lesnagekgla.lr..............keakekklegkeaelkdgavviaaitsctntsn 425
                                                       l+++ ++k+ + l+                  e+ +eg++++lk+gavviaaitsctntsn
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 397 lgLQVKPTSKEEGrLEseggggvavgnadqVGEAEYEFEGHTHRLKNGAVVIAAITSCTNTSN 459
                                                     445666566654314477788887877754345577889************************ PP

                                       TIGR01341 426 psvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGctt 488
                                                     psv+++agllakkave Gl +kp+vk+slapGskvvtdy + +gl++yl++lGf+lvGyGctt
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 460 PSVMMAAGLLAKKAVEKGLVRKPWVKSSLAPGSKVVTDYYNAAGLTEYLDKLGFDLVGYGCTT 522
                                                     *************************************************************** PP

                                       TIGR01341 489 ciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdi 551
                                                     ciGnsGpl++ +e+ai++ dl+v++vlsGnrnfegr+hplvk+n+laspplvvayalaGtv i
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 523 CIGNSGPLPDPIEKAIQKADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRI 585
                                                     *************************************************************** PP

                                       TIGR01341 552 dlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtss 614
                                                     d+++ep+g d+dGk+vyl+diwps +e+a++v  +v++ +f+key++v+ g+e+w+ +ev++ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 586 DISSEPLGNDRDGKPVYLRDIWPSSQEVAAAV-AQVNTSMFHKEYAAVFAGDEQWQAIEVPQA 647
                                                     *****************************955.689*************************** PP

                                       TIGR01341 615 dlyewdekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaak 677
                                                     ++y w+++styi++ppff+++   p  v +++gar+l+llGds+ttdhispaG+ik dspa++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 648 ATYVWQDDSTYIQHPPFFDDIGGPPPAVRNVEGARVLALLGDSVTTDHISPAGNIKADSPAGR 710
                                                     *************************************************************** PP

                                       TIGR01341 678 ylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaa 740
                                                     yl+e+Gve+rdfnsyGsrrGnh+vm+rGtfaniri+n++++g+eGg t+y+p +e + +ydaa
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 711 YLREQGVEPRDFNSYGSRRGNHQVMMRGTFANIRIRNEMLDGEEGGNTIYIPSGERMPIYDAA 773
                                                     *************************************************************** PP

                                       TIGR01341 741 mkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefk 803
                                                     m y+ +++plvv+aG+eyG+Gssrdwaakgt+llGvkaviaesferihrsnlvgmGvlpl+fk
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 774 MLYQATDTPLVVIAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFK 836
                                                     *************************************************************** PP

                                       TIGR01341 804 qgedaetlgltgeetidvddieel..kpkkevtvelvkedgeketveavlridtevelayvkk 864
                                                       +++++l+ltg+et+d+ +++++   p+ ++++++++edg +e +e+ +ridt  e++y+k 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 837 LDQNRKSLNLTGRETLDILGLNDVelTPRMNLPLVITREDGRQERIEVLCRIDTLNEVEYFKA 899
                                                     ******************999875227************************************ PP

                                       TIGR01341 865 gGilqyvlrkll 876
                                                     gGil+yvlr+l+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02385 900 GGILHYVLRQLI 911
                                                     *********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (913 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 0.04s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 8.37
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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