GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Pseudomonas fluorescens FW300-N2E3

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate AO353_00565 AO353_00565 aconitate hydratase

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



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 AO353_00565 aconitate
           hydratase
          Length = 916

 Score = 1300 bits (3364), Expect = 0.0
 Identities = 648/915 (70%), Positives = 748/915 (81%), Gaps = 8/915 (0%)

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

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

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

Query: 187 VNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPV 246
           VNLEYLG+TVW KD+D +T A+PDTLVGTDSHTTMINGLG+LGWGVGGIEAEAAMLGQPV
Sbjct: 183 VNLEYLGRTVWTKDEDDRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 242

Query: 247 SMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRAT 306
           SMLIPEV+GFK+TGKL+EGITATDLVLTVT+MLRKKGVVGKFVEFYGDGL ++P+ADRAT
Sbjct: 243 SMLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRAT 302

Query: 307 IANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDN 366
           IANMAPEYGATCGFFPVDE T++Y+RL+GR    ++LVEAY K QGLWR PG EPV+TD+
Sbjct: 303 IANMAPEYGATCGFFPVDEVTLEYLRLSGRPSAVVKLVEAYCKTQGLWRLPGQEPVFTDS 362

Query: 367 LELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAE---NREANLESEGGQ-T 422
           L LDM  VEASLAGPKRPQDRV+L N+  +F   +     PA      E  LESEGG   
Sbjct: 363 LALDMSSVEASLAGPKRPQDRVSLPNVAQAFTDFLGLQVKPARPTSKEEGRLESEGGGGV 422

Query: 423 AVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQK 482
           AVG  D     +    E  G+  RL  GAVVIAAITSCTNTSNPSVMMAAGL+A+KAV+K
Sbjct: 423 AVGNADLV---SEADYEYEGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEK 479

Query: 483 GLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEK 542
           GL  KPWVK+SLAPGSKVVTDY K  G    LD+LGF+LVGYGCTTCIGNSGPL + +EK
Sbjct: 480 GLKRKPWVKSSLAPGSKVVTDYYKAAGLTQYLDELGFSLVGYGCTTCIGNSGPLLEPIEK 539

Query: 543 AISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDK 602
           AI   DL VASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAG+VR+D+S +PLG  K
Sbjct: 540 AIQSSDLAVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGSVRMDISSEPLGEGK 599

Query: 603 DGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKS 662
           DG PVYL+D+WPS +EIA+AV +V T MF KEYAEVF GDA W++I+VP++  Y W   S
Sbjct: 600 DGKPVYLRDIWPSSKEIADAVAQVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQKDS 659

Query: 663 TYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHG 722
           TYIQHPPFF+ +      I DI  A ILALLGDSVTTDHISPAG+ K D+PAG+YL+E G
Sbjct: 660 TYIQHPPFFDDISGPLPVIQDISGARILALLGDSVTTDHISPAGNIKADSPAGRYLREQG 719

Query: 723 VEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKY 782
           VEP+DFNSYGSRRGNHEVMMRGTFAN+RIRNEML G EGG T ++PTGE++AIYDAAM+Y
Sbjct: 720 VEPRDFNSYGSRRGNHEVMMRGTFANIRIRNEMLGGEEGGNTLYIPTGEKLAIYDAAMRY 779

Query: 783 QEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFP 842
           Q  GTPLVVIAG+EYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+PLQF 
Sbjct: 780 QAAGTPLVVIAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFK 839

Query: 843 EGTDRKSLKLTGEETISIEGLSG-EIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVY 901
              +RKSL LTG+ET+ I+GL+G E+ P   L + +  +DGS+E  E+  RIDT NE  Y
Sbjct: 840 LDQNRKSLNLTGKETLDIQGLTGVELTPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEY 899

Query: 902 FKHGGILHYVVREML 916
           FK GGILHYV+R+++
Sbjct: 900 FKAGGILHYVLRQLI 914


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: 2300
Number of extensions: 98
Number of successful extensions: 4
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: 916
Length adjustment: 43
Effective length of query: 876
Effective length of database: 873
Effective search space:   764748
Effective search space used:   764748
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 AO353_00565 AO353_00565 (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.3185.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 1417.2   0.0          0 1416.9   0.0    1.1  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565  AO353_00565 aconitate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565  AO353_00565 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1416.9   0.0         0         0       1     876 []      18     914 ..      18     914 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1416.9 bits;  conditional E-value: 0
                                     TIGR01341   1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafk 65 
                                                   k+++y+sl+++++sl++++klp sl++lle++lr+ d+++++  d++al+ w ke  +d+ei+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565  18 KTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDEKTVTGADLKALAAWLKERRSDREIQYR 82 
                                                   689************************************************************** PP

                                     TIGR01341  66 parvvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanve 130
                                                   parv++qdftGvpavvdlaa+r a+++ g+dp++inpl+pvdlvidhsv vdk+ +++a+ +nv+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565  83 PARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSVMVDKFASSTAFTQNVD 147
                                                   ***************************************************************** PP

                                     TIGR01341 131 lefernkerykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtd 195
                                                   +e++rn ery+fl+w++ af n++vvppgtGi+hqvnleyl++ v+++++d +++a+pd+lvGtd
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 148 IEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQVNLEYLGRTVWTKDEDDRTYAFPDTLVGTD 212
                                                   ***************************************************************** PP

                                     TIGR01341 196 shttminGlGvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrk 260
                                                   shttminGlGvlGwGvGGieaeaa+lGqpvs+ +peviG+kltGkl+eG+tatdlvltvt++lrk
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 213 SHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRK 277
                                                   ***************************************************************** PP

                                     TIGR01341 261 kgvvgkfveffGeglkelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvek 325
                                                   kgvvgkfvef+G+gl+el+ladratianmapeyGat++ffp+d+vtl+ylrl+gr++  v+lve+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 278 KGVVGKFVEFYGDGLAELPLADRATIANMAPEYGATCGFFPVDEVTLEYLRLSGRPSAVVKLVEA 342
                                                   ***************************************************************** PP

                                     TIGR01341 326 ylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekgla 390
                                                   y+k+q+l++  ++ep++td + ld+s+veas+aGpkrpqdrv+l +v +af+  l  ++     +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 343 YCKTQGLWRLPGQEPVFTDSLALDMSSVEASLAGPKRPQDRVSLPNVAQAFTDFLGLQVKPARPT 407
                                                   ****************************************************9976554433322 PP

                                     TIGR01341 391 lr....................keakekklegkeaelkdgavviaaitsctntsnpsvllgagll 435
                                                    +                        ++  eg++++lk+gavviaaitsctntsnpsv+++agl+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 408 SKeegrleseggggvavgnadlVSEADYEYEGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLV 472
                                                   2224445688888888888766555667778********************************** PP

                                     TIGR01341 436 akkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeev 500
                                                   akkave Glk+kp+vk+slapGskvvtdy + +gl++yl+elGf+lvGyGcttciGnsGpl e +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 473 AKKAVEKGLKRKPWVKSSLAPGSKVVTDYYKAAGLTQYLDELGFSLVGYGCTTCIGNSGPLLEPI 537
                                                   ***************************************************************** PP

                                     TIGR01341 501 eeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGk 565
                                                   e+ai+ +dl v++vlsGnrnfegr+hplvk+n+laspplvvayalaG+v +d+++ep+g +kdGk
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 538 EKAIQSSDLAVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGSVRMDISSEPLGEGKDGK 602
                                                   ***************************************************************** PP

                                     TIGR01341 566 kvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyirepp 630
                                                   +vyl+diwps keia++v  +v + +f+key+ev+ g+++w+ +ev++ ++y w+++styi++pp
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 603 PVYLRDIWPSSKEIADAV-AQVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQKDSTYIQHPP 666
                                                   ****************65.689******************************************* PP

                                     TIGR01341 631 ffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsr 695
                                                   ff++++     ++di garil+llGds+ttdhispaG+ik dspa++yl+e+Gve+rdfnsyGsr
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 667 FFDDISGPLPVIQDISGARILALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEPRDFNSYGSR 731
                                                   *******88999***************************************************** PP

                                     TIGR01341 696 rGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGs 760
                                                   rGnhevm+rGtfaniri+n+++ g+eGg t+y+p++e++++ydaam+y+  g+plvv+aG+eyG+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 732 RGNHEVMMRGTFANIRIRNEMLGGEEGGNTLYIPTGEKLAIYDAAMRYQAAGTPLVVIAGQEYGT 796
                                                   ***************************************************************** PP

                                     TIGR01341 761 GssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddie 825
                                                   Gssrdwaakgt+llGvkaviaesferihrsnlvgmGvlpl+fk  +++++l+ltg+et+d+++++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 797 GSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTGKETLDIQGLT 861
                                                   ***************************************************************86 PP

                                     TIGR01341 826 ..elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
                                                     el p+ ++t+++++edg+ e ve+ +ridt  e++y+k gGil+yvlr+l+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 862 gvELTPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEYFKAGGILHYVLRQLI 914
                                                   33678*********************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (916 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 13.12
//
[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 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