GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_00565
          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.21772.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 0.03s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 13.06
//
[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