GapMind for catabolism of small carbon sources

 

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

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 Pf1N1B4_3821 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821
          Length = 864

 Score = 1439 bits (3724), Expect = 0.0
 Identities = 723/866 (83%), Positives = 780/866 (90%), Gaps = 7/866 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  RKPLPG+ LDYFD RAAV+AI PGAYD LPYTSRVLAENLVRRCDPATLT+SL Q
Sbjct: 1   MNTEFRKPLPGSHLDYFDVRAAVDAISPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
            + RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA+VNPVVP QLIVDH
Sbjct: 61  FIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVE GGFDP+AF KNRAIEDRRNEDRFHFI+WTK+AFKNVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVERGGFDPEAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVI   +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+ VGV
Sbjct: 181 SPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK QPGITATD+VLALTE+LRK+KVVGA+LEF GEGAS+LTLGDRATISNMAPEYGA
Sbjct: 241 ELTGKLQPGITATDMVLALTEYLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF+ID+QTIDYL+LTGR DEQ++LVE+YA+  GLWADSLK A+YER L FDLSSVVR
Sbjct: 301 TAAMFYIDQQTIDYLKLTGREDEQVQLVESYAKQTGLWADSLKGAQYERGLTFDLSSVVR 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 IAAGLLARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAGLTSELEQLGFGVVAFACTTC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAK AFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKNAFLASPPLVVAYAIAGTI 535

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

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
           V+PLYDWR  STYIRRPPYWEGALAG R LK +RPLAVL DNITTDHLSPSNAIML+SAA
Sbjct: 595 VAPLYDWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAA 654

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

Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
           +V+RMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN
Sbjct: 715 QVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 774

Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
           L+GMGVLPLEF+PG +R TL +DG+ETYDVIG+R PRATLTLV+NRKNGERVEVPVTCRL
Sbjct: 775 LVGMGVLPLEFQPGTDRHTLAIDGSETYDVIGDRTPRATLTLVINRKNGERVEVPVTCRL 834

Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESS 865
           D+ EEVSIYEAGGVL  FAQDFLE S
Sbjct: 835 DTAEEVSIYEAGGVLQRFAQDFLEES 860


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: 2217
Number of extensions: 81
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: 864
Length adjustment: 42
Effective length of query: 827
Effective length of database: 822
Effective search space:   679794
Effective search space used:   679794
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 Pf1N1B4_3821 (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.20650.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 1828.6   0.0          0 1828.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821  2-methylcitrate dehydratase FeS 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821  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 ! 1828.4   0.0         0         0       1     858 []       2     858 ..       2     858 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1828.4 bits;  conditional E-value: 0
                                      TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierk 64 
                                                    nt++rk+lpg++ldyfd raav+ai pgayd+lpytsrvlaenlvrr+dp+tl++slkq+ierk
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821   2 NTEFRKPLPGSHLDYFDVRAAVDAISPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQFIERK 65 
                                                    899************************************************************* PP

                                      TIGR02333  65 reldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggf 128
                                                    r+ldfpw+parvvchdilgqtalvdlaglrdaia +ggdpaqvnpvv+tqlivdhslave ggf
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821  66 RDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDHSLAVERGGF 129
                                                    **************************************************************** PP

                                      TIGR02333 129 dpdafeknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafp 192
                                                    dp+afeknraiedrrnedrfhfinwtkkafknvdvip+gngimhqinlekmspv+qv++gvafp
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 130 DPEAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKMSPVIQVRDGVAFP 193
                                                    **************************************************************** PP

                                      TIGR02333 193 dtlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivl 256
                                                    dt+vgtdshtphvdalgviaigvggleae+vmlgras+mrlp+ vgveltgk qpgitatd+vl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 194 DTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGVELTGKLQPGITATDMVL 257
                                                    **************************************************************** PP

                                      TIGR02333 257 alteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkltgre 320
                                                    alte+lrk+kvv+a+leffgega altlgdratisnm+peygataamf+id+qtidylkltgre
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 258 ALTEYLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGATAAMFYIDQQTIDYLKLTGRE 321
                                                    **************************************************************** PP

                                      TIGR02333 321 eeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiake 384
                                                    +eqv+lve+yak +glwadslk a+yer l+fdlssvvrn+agpsnphar+a sdlaakgi+++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 322 DEQVQLVESYAKQTGLWADSLKGAQYERGLTFDLSSVVRNMAGPSNPHARVAVSDLAAKGISGQ 385
                                                    **************************************************************** PP

                                      TIGR02333 385 veeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvk 448
                                                    +++++ g+mpdgaviiaaitsctntsnprnv+aagllarnanklgl+rkpwvksslapgsk+v 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 386 WDDVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANKLGLTRKPWVKSSLAPGSKTVA 448
                                                    *****.********************************************************** PP

                                      TIGR02333 449 lyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrih 512
                                                    lyl+eagl +ele+lgfg+vafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrih
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 449 LYLDEAGLTSELEQLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIH 512
                                                    **************************************************************** PP

                                      TIGR02333 513 pyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpe 576
                                                    pyak+aflaspplvvayaiagtirfdiekdvlgv +dgkeirlkdiwpsdeeidavv+a+vkpe
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 513 PYAKNAFLASPPLVVAYAIAGTIRFDIEKDVLGV-VDGKEIRLKDIWPSDEEIDAVVKASVKPE 575
                                                    **********************************.***************************** PP

                                      TIGR02333 577 qfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnitt 639
                                                    qfr+vyipmf+++ d++ kv+plydwr mstyirrppywegalag r lkgmrplavl+dnitt
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 576 QFRQVYIPMFAIHeDTGPKVAPLYDWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITT 639
                                                    ************989************************************************* PP

                                      TIGR02333 640 dhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvk 703
                                                    dhlspsnai+ldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemv+e+gkvk
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 640 DHLSPSNAIMLDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVK 703
                                                    **************************************************************** PP

                                      TIGR02333 704 qgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegf 767
                                                    qgslar+epeg+v+rmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveai aegf
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 704 QGSLARVEPEGQVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGF 767
                                                    **************************************************************** PP

                                      TIGR02333 768 erihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvt 831
                                                    erihrtnlvgmgvlplef+pgt+r+tla+dg+e+ydv+g++tpra+ltlv++rknge++evpvt
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 768 ERIHRTNLVGMGVLPLEFQPGTDRHTLAIDGSETYDVIGDRTPRATLTLVINRKNGERVEVPVT 831
                                                    **************************************************************** PP

                                      TIGR02333 832 crldtaeevsvyeaggvlqrfaqdfle 858
                                                    crldtaeevs+yeaggvlqrfaqdfle
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 832 CRLDTAEEVSIYEAGGVLQRFAQDFLE 858
                                                    *************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (858 nodes)
Target sequences:                          1  (864 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 12.85
//
[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