GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_6063 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)

Query= SwissProt::Q937N8
         (869 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 2-methylcitrate
           dehydratase FeS dependent (EC 4.2.1.79)
          Length = 863

 Score = 1452 bits (3758), Expect = 0.0
 Identities = 730/868 (84%), Positives = 785/868 (90%), Gaps = 7/868 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  RKPLPGT LDYFD R AV+AI+PGAYD LPYTSRVLAENLVRRCDPATL +SLLQ
Sbjct: 1   MNTEFRKPLPGTSLDYFDVREAVDAIRPGAYDGLPYTSRVLAENLVRRCDPATLRESLLQ 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 SLAVESGGSDPQAFAKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVI   +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+I+GV
Sbjct: 181 SPVIQQRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPEIIGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK QPGITATD+VLALTEFLRK+KVVGA+LEF GEGAS+LTLGDRATISNMAPEYGA
Sbjct: 241 ELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF+ID+QTIDYL+LTGR D+Q++LVETYA+ AGLWAD LK A+YER L FDLSSVVR
Sbjct: 301 TAAMFYIDQQTIDYLKLTGREDDQVRLVETYAKQAGLWADKLKGAQYERGLTFDLSSVVR 360

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

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA LLARNAN  GL RKPWVKSSLAPGSK V LYL+EA L  +LE+LGFG+VAFACTTC
Sbjct: 416 IAAGLLARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAGLTKELEQLGFGVVAFACTTC 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 LVGMGVLPLEFKPGTDRKTLGIDGSEIYDVIGERTPRATLTLVITRKNGERVEVPVTCRL 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: 82
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 Pf6N2E2_6063 (2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79))
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.30307.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 1836.2   0.0          0 1836.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063  2-methylcitrate dehydratase FeS 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063  2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1836.1   0.0         0         0       1     858 []       2     858 ..       2     858 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1836.1 bits;  conditional E-value: 0
                                      TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierk 64 
                                                    nt++rk+lpgt+ldyfd r+av+ai+pgayd lpytsrvlaenlvrr+dp+tl +sl qlierk
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063   2 NTEFRKPLPGTSLDYFDVREAVDAIRPGAYDGLPYTSRVLAENLVRRCDPATLRESLLQLIERK 65 
                                                    899************************************************************* PP

                                      TIGR02333  65 reldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggf 128
                                                    r+ldfpw+parvvchdilgqtalvdlaglrdaia +ggdpaqvnpvv+tqlivdhslave gg 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063  66 RDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDHSLAVESGGS 129
                                                    **************************************************************** PP

                                      TIGR02333 129 dpdafeknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafp 192
                                                    dp+af+knraiedrrnedrfhfinwtkkafknvdvip+gngimhqinlekmspv+q ++gvafp
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 130 DPQAFAKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKMSPVIQQRDGVAFP 193
                                                    **************************************************************** PP

                                      TIGR02333 193 dtlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivl 256
                                                    dt+vgtdshtphvdalgviaigvggleae+vmlgras+mrlp+i+gveltgk qpgitatd+vl
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 194 DTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPEIIGVELTGKLQPGITATDMVL 257
                                                    **************************************************************** PP

                                      TIGR02333 257 alteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkltgre 320
                                                    alteflrk+kvv+a+leffgega altlgdratisnm+peygataamf+id+qtidylkltgre
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 258 ALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGATAAMFYIDQQTIDYLKLTGRE 321
                                                    **************************************************************** PP

                                      TIGR02333 321 eeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiake 384
                                                    ++qv+lvetyak aglwad+lk a+yer l+fdlssvvrn+agpsnphar+a sdlaakgi+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 322 DDQVRLVETYAKQAGLWADKLKGAQYERGLTFDLSSVVRNMAGPSNPHARVAVSDLAAKGISGQ 385
                                                    **************************************************************** PP

                                      TIGR02333 385 veeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvk 448
                                                    +++++ g+mpdgaviiaaitsctntsnprnv+aagllarnanklgl+rkpwvksslapgsk+v 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 386 WDDVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANKLGLTRKPWVKSSLAPGSKTVA 448
                                                    *****.********************************************************** PP

                                      TIGR02333 449 lyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrih 512
                                                    lyl+eagl kele+lgfg+vafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrih
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 449 LYLDEAGLTKELEQLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIH 512
                                                    **************************************************************** PP

                                      TIGR02333 513 pyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpe 576
                                                    pyakqaflaspplvvayaiagtirfdiekdvlgv +dg+eirlkdiwpsdeeidavv+a+vkpe
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 513 PYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGV-VDGREIRLKDIWPSDEEIDAVVKASVKPE 575
                                                    **********************************.***************************** PP

                                      TIGR02333 577 qfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnitt 639
                                                    qfr+vyipmf+++ d++ kv+plydwrp+styirrppywegalag r lkgmrplavl+dnitt
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 576 QFRQVYIPMFAIQeDTGPKVTPLYDWRPQSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITT 639
                                                    ************989************************************************* PP

                                      TIGR02333 640 dhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvk 703
                                                    dhlspsnai+ldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemv+e+gkvk
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 640 DHLSPSNAIMLDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVK 703
                                                    **************************************************************** PP

                                      TIGR02333 704 qgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegf 767
                                                    qgslar+epegkv+rmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveai aegf
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 704 QGSLARVEPEGKVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGF 767
                                                    **************************************************************** PP

                                      TIGR02333 768 erihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvt 831
                                                    erihrtnlvgmgvlplefkpgt+rktl++dg+e+ydv+ge+tpra+ltlv+trknge++evpvt
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 768 ERIHRTNLVGMGVLPLEFKPGTDRKTLGIDGSEIYDVIGERTPRATLTLVITRKNGERVEVPVT 831
                                                    **************************************************************** PP

                                      TIGR02333 832 crldtaeevsvyeaggvlqrfaqdfle 858
                                                    crldtaeevs+yeaggvlqrfaqdfle
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6063 832 CRLDTAEEVSIYEAGGVLQRFAQDFLE 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 7.90
//
[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 paper from 2022 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