GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Pseudomonas fluorescens FW300-N2C3

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 AO356_20875 AO356_20875 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= SwissProt::Q937N8
         (869 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 AO356_20875
           Fe/S-dependent 2-methylisocitrate dehydratase AcnD
          Length = 863

 Score = 1451 bits (3757), Expect = 0.0
 Identities = 732/868 (84%), Positives = 783/868 (90%), Gaps = 7/868 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  RKPLPGT LDYFD R AV+AI+PGAYD LPYTSRVLAENLVRRCDPATL +SLLQ
Sbjct: 1   MNTEFRKPLPGTSLDYFDVRGAVDAIRPGAYDGLPYTSRVLAENLVRRCDPATLRESLLQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           L+ RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA+VNPVVP QLIVDH
Sbjct: 61  LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVE GG DP AFAKNRAIEDRRNEDRFHFI+WTK+AFKNVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVESGGADPQAFAKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVI   +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+IVGV
Sbjct: 181 SPVIQQRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPEIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK QPGITATD+VLALTEFLRK+KVVGA+LEF GEGAS+LTLGDR TISNMAPEYGA
Sbjct: 241 ELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRVTISNMAPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF ID+QTIDYL+LTGR D Q++LVETYA+  GLWADSLK A+YER L FDLSSVVR
Sbjct: 301 TAAMFHIDQQTIDYLKLTGREDTQVQLVETYAKHVGLWADSLKGAQYERGLTFDLSSVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
           NMAGPSNPH R+  S LA +GI+   D     +  G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHARVAVSELAAKGISGQWD-----DVPGQMPDGAVIIAAITSCTNTSNPRNV 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA LLARNAN  GLARKPWVKSSLAPGSK V LYL+EA L  +LEKLGFG+VAFACTTC
Sbjct: 416 IAAGLLARNANRLGLARKPWVKSSLAPGSKTVALYLDEAGLTSELEKLGFGVVAFACTTC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLG   DG+ + LKDIWPSDEEIDA+V  SVKPEQFR+VY PMFAI   +G  
Sbjct: 536 RFDIEKDVLGV-VDGREIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIQEDTGPK 594

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
           V+PLYDWRPQSTYIRRPPYWEGALAG R LK +RPLAVL DNITTDHLSPSNAIML+SAA
Sbjct: 595 VTPLYDWRPQSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAA 654

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM   +G+VK+GSLAR+EPEG
Sbjct: 655 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVKQGSLARVEPEG 714

Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
           KV+RMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN
Sbjct: 715 KVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 774

Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
           L+GMGVLPLEFKPG +R TLG+DG+E YDVIGER PRATLTLV+ RKNGERVEVPVTCRL
Sbjct: 775 LVGMGVLPLEFKPGTDRKTLGIDGSEVYDVIGERTPRATLTLVITRKNGERVEVPVTCRL 834

Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRA 867
           D+ EEVSIYEAGGVL  FAQDFLES+ A
Sbjct: 835 DTAEEVSIYEAGGVLQRFAQDFLESAVA 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: 2210
Number of extensions: 84
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: 863
Length adjustment: 42
Effective length of query: 827
Effective length of database: 821
Effective search space:   678967
Effective search space used:   678967
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 AO356_20875 AO356_20875 (Fe/S-dependent 2-methylisocitrate dehydratase AcnD)
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.11003.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 1826.9   0.0          0 1826.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875  AO356_20875 Fe/S-dependent 2-met


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875  AO356_20875 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1826.7   0.0         0         0       1     858 []       2     858 ..       2     858 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1826.7 bits;  conditional E-value: 0
                                       TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlier 63 
                                                     nt++rk+lpgt+ldyfd r av+ai+pgayd lpytsrvlaenlvrr+dp+tl +sl qlier
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875   2 NTEFRKPLPGTSLDYFDVRGAVDAIRPGAYDGLPYTSRVLAENLVRRCDPATLRESLLQLIER 64 
                                                     899************************************************************ PP

                                       TIGR02333  64 kreldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyg 126
                                                     kr+ldfpw+parvvchdilgqtalvdlaglrdaia +ggdpaqvnpvv+tqlivdhslave g
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875  65 KRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDHSLAVESG 127
                                                     *************************************************************** PP

                                       TIGR02333 127 gfdpdafeknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegv 189
                                                     g dp+af+knraiedrrnedrfhfinwtkkafknvdvip+gngimhqinlekmspv+q ++gv
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 128 GADPQAFAKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKMSPVIQQRDGV 190
                                                     *************************************************************** PP

                                       TIGR02333 190 afpdtlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitat 252
                                                     afpdt+vgtdshtphvdalgviaigvggleae+vmlgras+mrlp+ivgveltgk qpgitat
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 191 AFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPEIVGVELTGKLQPGITAT 253
                                                     *************************************************************** PP

                                       TIGR02333 253 divlalteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylk 315
                                                     d+vlalteflrk+kvv+a+leffgega altlgdr tisnm+peygataamf id+qtidylk
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 254 DMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRVTISNMAPEYGATAAMFHIDQQTIDYLK 316
                                                     *************************************************************** PP

                                       TIGR02333 316 ltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaa 378
                                                     ltgre+ qv+lvetyak  glwadslk a+yer l+fdlssvvrn+agpsnphar+a s+laa
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 317 LTGREDTQVQLVETYAKHVGLWADSLKGAQYERGLTFDLSSVVRNMAGPSNPHARVAVSELAA 379
                                                     *************************************************************** PP

                                       TIGR02333 379 kgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvkssla 441
                                                     kgi++++++++ g+mpdgaviiaaitsctntsnprnv+aagllarnan+lgl rkpwvkssla
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 380 KGISGQWDDVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANRLGLARKPWVKSSLA 441
                                                     ***********.*************************************************** PP

                                       TIGR02333 442 pgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgn 504
                                                     pgsk+v lyl+eagl +eleklgfg+vafacttcngmsgaldpviqqeiidrdlyatavlsgn
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 442 PGSKTVALYLDEAGLTSELEKLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGN 504
                                                     *************************************************************** PP

                                       TIGR02333 505 rnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeida 567
                                                     rnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgv +dg+eirlkdiwpsdeeida
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 505 RNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGV-VDGREIRLKDIWPSDEEIDA 566
                                                     ******************************************.******************** PP

                                       TIGR02333 568 vvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrp 629
                                                     vv+a+vkpeqfr+vyipmf+++ d++ kv+plydwrp+styirrppywegalag r lkgmrp
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 567 VVKASVKPEQFRQVYIPMFAIQeDTGPKVTPLYDWRPQSTYIRRPPYWEGALAGARPLKGMRP 629
                                                     *********************989*************************************** PP

                                       TIGR02333 630 lavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklf 692
                                                     lavl+dnittdhlspsnai+ldsaageylakmglpeedfnsyathrgdhltaqratfanpklf
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 630 LAVLPDNITTDHLSPSNAIMLDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLF 692
                                                     *************************************************************** PP

                                       TIGR02333 693 nemvkedgkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvr 755
                                                     nemv+e+gkvkqgslar+epegkv+rmweaietym+rkqpliiiagadygqgssrdwaakgvr
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 693 NEMVQENGKVKQGSLARVEPEGKVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVR 755
                                                     *************************************************************** PP

                                       TIGR02333 756 lagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvv 818
                                                     lagveai aegferihrtnlvgmgvlplefkpgt+rktl++dg+evydv+ge+tpra+ltlv+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 756 LAGVEAIAAEGFERIHRTNLVGMGVLPLEFKPGTDRKTLGIDGSEVYDVIGERTPRATLTLVI 818
                                                     *************************************************************** PP

                                       TIGR02333 819 trkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
                                                     trknge++evpvtcrldtaeevs+yeaggvlqrfaqdfle
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 819 TRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 858
                                                     **************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (858 nodes)
Target sequences:                          1  (863 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: 8.43
//
[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