GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS11425
          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.17587.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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 12.99
//
[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