GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Pseudomonas fluorescens FW300-N1B4

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate Pf1N1B4_3888 Aconitate hydratase (EC 4.2.1.3)

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 Aconitate hydratase
           (EC 4.2.1.3)
          Length = 913

 Score = 1311 bits (3394), Expect = 0.0
 Identities = 649/916 (70%), Positives = 755/916 (82%), Gaps = 13/916 (1%)

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

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

Query: 127 VDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQ 186
           VDLVIDHSVMVDK+  AS+F  NV IEM+RN ERY FLRWGQ AF+NF VVPPGTGICHQ
Sbjct: 123 VDLVIDHSVMVDKYASASAFGQNVDIEMQRNHERYAFLRWGQSAFNNFSVVPPGTGICHQ 182

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

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

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

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

Query: 426 ----VDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQ 481
               + ++  HH        G   RL  GAVVIAAITSCTNTSNPSVMMAAGL+A+KAV+
Sbjct: 423 NADLIGEADYHH-------EGSTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVE 475

Query: 482 KGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVE 541
           KGL  KPWVK+SLAPGSKVVTDY K  G    LD+LGF LVGYGCTTCIGNSGPLP+ +E
Sbjct: 476 KGLKRKPWVKSSLAPGSKVVTDYYKAAGLTQYLDELGFALVGYGCTTCIGNSGPLPEPIE 535

Query: 542 KAISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGND 601
           KAI   DLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAG VR+D+S +PLGND
Sbjct: 536 KAIQKADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGND 595

Query: 602 KDGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDK 661
           KDG+PVYL+D+WPS +EIA+AV +V T MF KEYAEVF GD  W++I+VP++  Y W++ 
Sbjct: 596 KDGHPVYLRDIWPSTKEIADAVTQVNTAMFHKEYAEVFAGDEQWQAIEVPQAATYVWNND 655

Query: 662 STYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEH 721
           STYIQHPPFF+ +      + D++ A +LALLGDSVTTDHISPAG+ K D+PAG YL+E 
Sbjct: 656 STYIQHPPFFDDIGGPAPVVKDVEGAKVLALLGDSVTTDHISPAGNIKADSPAGHYLREQ 715

Query: 722 GVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMK 781
           GVEP+DFNSYGSRRGNH+VMMRGTFAN+RIRNEML G EGG T ++PTGE++ IYDAAM+
Sbjct: 716 GVEPRDFNSYGSRRGNHQVMMRGTFANIRIRNEMLGGEEGGNTIYIPTGEKLPIYDAAMR 775

Query: 782 YQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQF 841
           YQ  GTPLVVIAG+EYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+PLQF
Sbjct: 776 YQASGTPLVVIAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQF 835

Query: 842 PEGTDRKSLKLTGEETISIEGLSG-EIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAV 900
               +RKSL LTG+ET+ I GL+G E+ P   L + V  +DG+TE  E+  RIDT NE  
Sbjct: 836 KLDQNRKSLNLTGKETLDILGLTGVELTPRMNLTLVVTREDGNTEKVEVLCRIDTLNEVE 895

Query: 901 YFKHGGILHYVVREML 916
           YFK GGILHYV+R+++
Sbjct: 896 YFKAGGILHYVLRQLI 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: 2370
Number of extensions: 104
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 Pf1N1B4_3888 (Aconitate hydratase (EC 4.2.1.3))
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.16686.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 1420.5   0.0          0 1420.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888  Aconitate hydratase (EC 4.2.1.3)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888  Aconitate hydratase (EC 4.2.1.3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1420.2   0.0         0         0       1     876 []      18     911 ..      18     911 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1420.2 bits;  conditional E-value: 0
                                      TIGR01341   1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiaf 64 
                                                    k+++y+sl+++++sl++++klp sl++lle++lr+ d+++++  d++a++ w ke  +d+ei++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888  18 KTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDEKTVTGADLKAIAAWLKERRSDREIQY 81 
                                                    689************************************************************* PP

                                      TIGR01341  65 kparvvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealean 128
                                                    +parv++qdftGvpavvdlaa+r a+++ g+dp++inpl+pvdlvidhsv vdk+ + +a+ +n
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888  82 RPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSVMVDKYASASAFGQN 145
                                                    **************************************************************** PP

                                      TIGR01341 129 velefernkerykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslv 192
                                                    v++e++rn+ery+fl+w++ af+n++vvppgtGi+hqvnleyl++ v+++++dg+++a+pd+lv
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 146 VDIEMQRNHERYAFLRWGQSAFNNFSVVPPGTGICHQVNLEYLGRTVWTKDEDGRTYAFPDTLV 209
                                                    **************************************************************** PP

                                      TIGR01341 193 GtdshttminGlGvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvte 256
                                                    GtdshttminGlGvlGwGvGGieaeaa+lGqpvs+ +peviG+kltGkl+eG+tatdlvltvt+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 210 GTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLTGKLKEGITATDLVLTVTQ 273
                                                    **************************************************************** PP

                                      TIGR01341 257 llrkkgvvgkfveffGeglkelsladratianmapeyGataaffpiddvtlqylrltgrdedkv 320
                                                    +lrkkgvvgkfvef+G+gl+ l+ladratianmapeyGat++ffp+d+vtl+ylrl+gr  ++v
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 274 MLRKKGVVGKFVEFYGDGLADLPLADRATIANMAPEYGATCGFFPVDEVTLEYLRLSGRTPQTV 337
                                                    **************************************************************** PP

                                      TIGR01341 321 elvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafkss..les 382
                                                    +lve+y k+q+l++  ++ep++td + ld+ +veas+aGpkrpqdrv+l +v +af+    l+ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 338 KLVEAYSKTQGLWRLPGKEPVFTDSLALDMGSVEASLAGPKRPQDRVSLPNVAQAFTDFlgLQF 401
                                                    ********************************************************99844444 PP

                                      TIGR01341 383 nagekg.lalr..............keakekklegkeaelkdgavviaaitsctntsnpsvllg 431
                                                    + ++k+   l+                  +++ eg++++lk+gavviaaitsctntsnpsv+++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 402 KPSSKEeGRLEseggggvavgnadlIGEADYHHEGSTYRLKNGAVVIAAITSCTNTSNPSVMMA 465
                                                    4444430334466677766666655344566668****************************** PP

                                      TIGR01341 432 agllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGp 495
                                                    agl+akkave Glk+kp+vk+slapGskvvtdy + +gl++yl+elGf lvGyGcttciGnsGp
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 466 AGLVAKKAVEKGLKRKPWVKSSLAPGSKVVTDYYKAAGLTQYLDELGFALVGYGCTTCIGNSGP 529
                                                    **************************************************************** PP

                                      TIGR01341 496 leeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepig 559
                                                    l+e +e+ai++ dl+v++vlsGnrnfegr+hplvk+n+laspplvvayalaGtv id+++ep+g
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 530 LPEPIEKAIQKADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLG 593
                                                    **************************************************************** PP

                                      TIGR01341 560 tdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdeks 623
                                                     dkdG++vyl+diwps+keia++v ++v++ +f+key+ev+ g+e+w+ +ev++ ++y w+++s
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 594 NDKDGHPVYLRDIWPSTKEIADAV-TQVNTAMFHKEYAEVFAGDEQWQAIEVPQAATYVWNNDS 656
                                                    **********************65.689************************************ PP

                                      TIGR01341 624 tyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverr 687
                                                    tyi++ppff+++      v+d++ga++l+llGds+ttdhispaG+ik dspa++yl+e+Gve+r
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 657 TYIQHPPFFDDIGGPAPVVKDVEGAKVLALLGDSVTTDHISPAGNIKADSPAGHYLREQGVEPR 720
                                                    *************988999********************************************* PP

                                      TIGR01341 688 dfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplv 751
                                                    dfnsyGsrrGnh+vm+rGtfaniri+n+++ g+eGg t+y+p++e++ +ydaam+y+ +g+plv
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 721 DFNSYGSRRGNHQVMMRGTFANIRIRNEMLGGEEGGNTIYIPTGEKLPIYDAAMRYQASGTPLV 784
                                                    **************************************************************** PP

                                      TIGR01341 752 vlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltg 815
                                                    v+aG+eyG+Gssrdwaakgt+llGvkaviaesferihrsnlvgmGvlpl+fk  +++++l+ltg
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 785 VIAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTG 848
                                                    **************************************************************** PP

                                      TIGR01341 816 eetidvddie..elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
                                                    +et+d+ +++  el p+ ++t+++++edg+ e ve+ +ridt  e++y+k gGil+yvlr+l+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 849 KETLDILGLTgvELTPRMNLTLVVTREDGNTEKVEVLCRIDTLNEVEYFKAGGILHYVLRQLI 911
                                                    ******998633688*********************************************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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 8.87
//
[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