GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Herbaspirillum seropedicae SmR1

Align Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate HSERO_RS11425 HSERO_RS11425 aconitate hydratase

Query= SwissProt::Q937N8
         (869 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS11425 HSERO_RS11425 aconitate
           hydratase
          Length = 873

 Score = 1476 bits (3821), Expect = 0.0
 Identities = 739/867 (85%), Positives = 790/867 (91%), Gaps = 7/867 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  RK LPGT+LDYFDARAAVEAI+PGA+D LPYTSRVLAENLVRRCDPATLTDSL Q
Sbjct: 1   MNTQYRKQLPGTRLDYFDARAAVEAIRPGAWDTLPYTSRVLAENLVRRCDPATLTDSLRQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           L+ RKR+LDFPWFPARVVCHDILGQTALVDLAGLRDAIAD GGDPAKVNPVVPVQLIVDH
Sbjct: 61  LIERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIADMGGDPAKVNPVVPVQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGG DP AF KNRAIEDRRNEDRFHFIDWTK AF+NVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVECGGDDPQAFVKNRAIEDRRNEDRFHFIDWTKLAFENVDVIPPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVIHA +GVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDI+GV
Sbjct: 181 SPVIHAKDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIIGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTG+RQPGITATDIVL+LTEFLRK+KVVGAYLEF G+GA+SLTLGDRATISNMAPEYGA
Sbjct: 241 ELTGRRQPGITATDIVLSLTEFLRKQKVVGAYLEFYGDGAASLTLGDRATISNMAPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF ID+QTIDYL+LTGR DEQ+KLVETYA+ AGLW+D+L   EYERVL+FDLS+VVR
Sbjct: 301 TAAMFSIDQQTIDYLKLTGREDEQVKLVETYAKEAGLWSDTLAKVEYERVLRFDLSTVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
            +AGPSNPHKRLP S LA +GIA        +   G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 TLAGPSNPHKRLPVSELAAQGIA-----GKVENEPGKMPDGAVIIAAITSCTNTSNPRNV 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA LLARNAN  GLARKPWVKSSLAPGSKAVELYLEEA L  DLEKLGFGIVAFACTTC
Sbjct: 416 IAAGLLARNANRLGLARKPWVKSSLAPGSKAVELYLEEAGLTADLEKLGFGIVAFACTTC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDPKIQQEIIDRDLY+TAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPKIQQEIIDRDLYSTAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIE+DVLG   +G+ + LKDIWPSDEEIDA+V  +VKP+QFR VY PMFA      +S
Sbjct: 536 RFDIEQDVLGVTAEGREIRLKDIWPSDEEIDAVVTAAVKPQQFRNVYTPMFAARVDRSQS 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
           VSPLYDWRPQSTYIRRPPYWEGALAGERTL  +RPLAVLGDNITTDHLSPSNAI+L+SAA
Sbjct: 596 VSPLYDWRPQSTYIRRPPYWEGALAGERTLSGMRPLAVLGDNITTDHLSPSNAILLDSAA 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMA-VVDGQVKKGSLARIEPE 719
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM    DG V++GSLAR+EPE
Sbjct: 656 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVKKADGSVQQGSLARLEPE 715

Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
           GKV+RMWE IETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRT
Sbjct: 716 GKVMRMWETIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 775

Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
           NLIGMGVLPLEFK G NR T  +DGTETYDVIG+R+PRA LTLV++RKNGERVEVPVTCR
Sbjct: 776 NLIGMGVLPLEFKAGENRNTYAIDGTETYDVIGQRRPRADLTLVIHRKNGERVEVPVTCR 835

Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESS 865
           LD+ EEVSIYEAGGVL  FAQDFLE+S
Sbjct: 836 LDTAEEVSIYEAGGVLQRFAQDFLEAS 862


Lambda     K      H
   0.318    0.135    0.398 

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: 2276
Number of extensions: 102
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: 869
Length of database: 873
Length adjustment: 42
Effective length of query: 827
Effective length of database: 831
Effective search space:   687237
Effective search space used:   687237
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 (21.7 bits)
S2: 56 (26.2 bits)

Align candidate HSERO_RS11425 HSERO_RS11425 (aconitate hydratase)
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))

# 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/TIGR02333.hmm
# target sequence database:        /tmp/gapView.2142.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02333  [M=858]
Accession:   TIGR02333
Description: 2met_isocit_dHY: 2-methylisocitrate dehydratase, Fe/S-dependent
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 1816.5   0.0          0 1816.3   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS11425  HSERO_RS11425 aconitate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS11425  HSERO_RS11425 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1816.3   0.0         0         0       1     858 []       2     860 ..       2     860 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1816.3 bits;  conditional E-value: 0
                                  TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreld 68 
                                                nt+yrk+lpgt ldyfdaraaveai+pga+d+lpytsrvlaenlvrr+dp+tl++sl+qlierkreld
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425   2 NTQYRKQLPGTRLDYFDARAAVEAIRPGAWDTLPYTSRVLAENLVRRCDPATLTDSLRQLIERKRELD 69 
                                                89****************************************************************** PP

                                  TIGR02333  69 fpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafekn 136
                                                fpw+parvvchdilgqtalvdlaglrdaia+ ggdpa+vnpvv++qlivdhslave+gg dp+af kn
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425  70 FPWFPARVVCHDILGQTALVDLAGLRDAIADMGGDPAKVNPVVPVQLIVDHSLAVECGGDDPQAFVKN 137
                                                ******************************************************************** PP

                                  TIGR02333 137 raiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtph 204
                                                raiedrrnedrfhfi+wtk af+nvdvip+gngimhqinlekmspv+++k+gvafpdtlvgtdshtph
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425 138 RAIEDRRNEDRFHFIDWTKLAFENVDVIPPGNGIMHQINLEKMSPVIHAKDGVAFPDTLVGTDSHTPH 205
                                                ******************************************************************** PP

                                  TIGR02333 205 vdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayl 272
                                                vdalgviaigvggleae+vmlgras+mrlpdi+gveltg+rqpgitatdivl+lteflrk+kvv+ayl
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425 206 VDALGVIAIGVGGLEAENVMLGRASWMRLPDIIGVELTGRRQPGITATDIVLSLTEFLRKQKVVGAYL 273
                                                ******************************************************************** PP

                                  TIGR02333 273 effgegakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwads 340
                                                ef+g+ga +ltlgdratisnm+peygataamf id+qtidylkltgre+eqvklvetyak aglw+d+
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425 274 EFYGDGAASLTLGDRATISNMAPEYGATAAMFSIDQQTIDYLKLTGREDEQVKLVETYAKEAGLWSDT 341
                                                ******************************************************************** PP

                                  TIGR02333 341 lkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeaeglmpdgaviiaaitsctn 408
                                                l k +yervl+fdls+vvr+lagpsnph+rl+ s+laa+gia++ve+e+ g+mpdgaviiaaitsctn
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425 342 LAKVEYERVLRFDLSTVVRTLAGPSNPHKRLPVSELAAQGIAGKVENEP-GKMPDGAVIIAAITSCTN 408
                                                *************************************************.****************** PP

                                  TIGR02333 409 tsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafacttcn 476
                                                tsnprnv+aagllarnan+lgl rkpwvksslapgsk+v+lyleeagl ++leklgfgivafacttcn
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425 409 TSNPRNVIAAGLLARNANRLGLARKPWVKSSLAPGSKAVELYLEEAGLTADLEKLGFGIVAFACTTCN 476
                                                ******************************************************************** PP

                                  TIGR02333 477 gmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvl 544
                                                gmsgaldp+iqqeiidrdly+tavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdie+dvl
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425 477 GMSGALDPKIQQEIIDRDLYSTAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEQDVL 544
                                                ******************************************************************** PP

                                  TIGR02333 545 gvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrp 611
                                                gv a+g+eirlkdiwpsdeeidavv+aavkp+qfr+vy pmf+   d++++vsplydwrp+styirrp
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425 545 GVTAEGREIRLKDIWPSDEEIDAVVTAAVKPQQFRNVYTPMFAARvDRSQSVSPLYDWRPQSTYIRRP 612
                                                *******************************************999********************** PP

                                  TIGR02333 612 pywegalagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhl 679
                                                pywegalagertl gmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhl
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425 613 PYWEGALAGERTLSGMRPLAVLGDNITTDHLSPSNAILLDSAAGEYLAKMGLPEEDFNSYATHRGDHL 680
                                                ******************************************************************** PP

                                  TIGR02333 680 taqratfanpklfnemvked.gkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgss 746
                                                taqratfanpklfnemvk+  g+v+qgslar+epegkv+rmwe+ietym+rkqpliiiagadygqgss
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425 681 TAQRATFANPKLFNEMVKKAdGSVQQGSLARLEPEGKVMRMWETIETYMERKQPLIIIAGADYGQGSS 748
                                                *****************9766*********************************************** PP

                                  TIGR02333 747 rdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradl 814
                                                rdwaakgvrlagveaivaegferihrtnl+gmgvlplefk+g+nr+t+a+dgte+ydv+g+++pradl
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425 749 RDWAAKGVRLAGVEAIVAEGFERIHRTNLIGMGVLPLEFKAGENRNTYAIDGTETYDVIGQRRPRADL 816
                                                ******************************************************************** PP

                                  TIGR02333 815 tlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
                                                tlv++rknge++evpvtcrldtaeevs+yeaggvlqrfaqdfle
  lcl|FitnessBrowser__HerbieS:HSERO_RS11425 817 TLVIHRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 860
                                                ******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (858 nodes)
Target sequences:                          1  (873 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 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.50
//
[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