GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Shewanella amazonensis SB2B

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 6939202 Sama_3296 aconitate hydratase (RefSeq)

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__SB2B:6939202
          Length = 861

 Score = 1407 bits (3641), Expect = 0.0
 Identities = 703/867 (81%), Positives = 768/867 (88%), Gaps = 8/867 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  RKPLPGT L +FD R AV+AI PGA+DKLPYTS+VLAENL+R+ +PA L D L Q
Sbjct: 1   MNTQFRKPLPGTNLSFFDTREAVDAIAPGAFDKLPYTSKVLAENLLRKAEPARLNDFLSQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           L+ RK+DLDFPWFPARVVCHDILGQTALVDLAGLRDAIA +GGDPAKVNPVVP QLIVDH
Sbjct: 61  LIFRKQDLDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAKVNPVVPTQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVE GGF+ DAF KNRAIEDRRN+DRFHFI+WTK+AF+NVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVEHGGFEKDAFEKNRAIEDRRNDDRFHFINWTKKAFRNVDVIPPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVI   +G+A+PDTCVGTDSHTPHVD+LGVIAIGVGGLEAENVMLGRASWMRLPDIVGV
Sbjct: 181 SPVIQVRDGIAFPDTCVGTDSHTPHVDSLGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK  PGITATD+VLALTEFLRKE+VVGAYLEF GEGA +LTLGDRATISNM PEYGA
Sbjct: 241 ELTGKPNPGITATDVVLALTEFLRKERVVGAYLEFFGEGAKALTLGDRATISNMTPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF+IDEQTIDYLRLTGR ++Q++LVE YA+T GLWAD++  A+Y R+L FDLSSVVR
Sbjct: 301 TAAMFYIDEQTIDYLRLTGRDEKQVELVENYAKTTGLWADAMTGADYGRILTFDLSSVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
           NMAGPSNPH RL TS LA +GIA D      QE  G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHARLATSDLAAKGIAADW-----QEESGKMPDGAVIIAAITSCTNTSNPRNV 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA L+ARNA  +GL RKPWVK+SLAPGSKAVELYL+EA LLP LE+LGFGIVAFACTTC
Sbjct: 416 IAAGLIARNAVQKGLVRKPWVKTSLAPGSKAVELYLKEAGLLPYLEQLGFGIVAFACTTC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQQEII+RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT+
Sbjct: 476 NGMSGALDPVIQQEIIERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTV 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLG D  G  V LKD+WP D EIDAI+  SVKPEQFR VY+PMF +    G +
Sbjct: 536 RFDIEKDVLGIDDAGNAVTLKDLWPEDAEIDAIIKSSVKPEQFRAVYDPMFNLAVEYG-T 594

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
             PLYDWRPQSTYIRRPPYWEGALAGERTL  +RPLAVLGDNITTDHLSPSNAI+ +SAA
Sbjct: 595 EKPLYDWRPQSTYIRRPPYWEGALAGERTLSGMRPLAVLGDNITTDHLSPSNAILASSAA 654

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAV-VDGQVKKGSLARIEPE 719
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM    DG+VK+GSLAR+EPE
Sbjct: 655 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVKDADGKVKQGSLARLEPE 714

Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
           GKV+RMWE IETYM+RKQPLII+AG DYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT
Sbjct: 715 GKVLRMWETIETYMERKQPLIIVAGKDYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 774

Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
           NL+GMGVLPLEF PG  R+T G+DGTET+DV GER P A LTL++ R+NGE VEVPV CR
Sbjct: 775 NLVGMGVLPLEFMPGETRMTYGIDGTETFDVKGERTPGAELTLLIRRQNGETVEVPVRCR 834

Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESS 865
           LD+ EEVSIYEAGGVL  FAQDFL +S
Sbjct: 835 LDTAEEVSIYEAGGVLQRFAQDFLANS 861


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: 2229
Number of extensions: 96
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: 861
Length adjustment: 42
Effective length of query: 827
Effective length of database: 819
Effective search space:   677313
Effective search space used:   677313
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 6939202 Sama_3296 (aconitate hydratase (RefSeq))
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.31567.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 1770.0   0.0          0 1769.8   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6939202  Sama_3296 aconitate hydratase (R


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939202  Sama_3296 aconitate hydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1769.8   0.0         0         0       1     858 []       2     859 ..       2     859 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1769.8 bits;  conditional E-value: 0
                         TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyparvv 77 
                                       nt++rk+lpgt+l +fd+r+av+ai+pga+dklpyts+vlaenl+r+++p++l+++l+qli rk++ldfpw+parvv
  lcl|FitnessBrowser__SB2B:6939202   2 NTQFRKPLPGTNLSFFDTREAVDAIAPGAFDKLPYTSKVLAENLLRKAEPARLNDFLSQLIFRKQDLDFPWFPARVV 78 
                                       89*************************************************************************** PP

                         TIGR02333  78 chdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhfinwt 154
                                       chdilgqtalvdlaglrdaia+kggdpa+vnpvv+tqlivdhslave ggf++dafeknraiedrrn+drfhfinwt
  lcl|FitnessBrowser__SB2B:6939202  79 CHDILGQTALVDLAGLRDAIAAKGGDPAKVNPVVPTQLIVDHSLAVEHGGFEKDAFEKNRAIEDRRNDDRFHFINWT 155
                                       ***************************************************************************** PP

                         TIGR02333 155 kkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvmlgraslm 231
                                       kkaf+nvdvip+gngimhqinlekmspv+qv++g+afpdt+vgtdshtphvd+lgviaigvggleae+vmlgras+m
  lcl|FitnessBrowser__SB2B:6939202 156 KKAFRNVDVIPPGNGIMHQINLEKMSPVIQVRDGIAFPDTCVGTDSHTPHVDSLGVIAIGVGGLEAENVMLGRASWM 232
                                       ***************************************************************************** PP

                         TIGR02333 232 rlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaide 308
                                       rlpdivgveltgk +pgitatd+vlalteflrke+vv+ayleffgegakaltlgdratisnmtpeygataamf+ide
  lcl|FitnessBrowser__SB2B:6939202 233 RLPDIVGVELTGKPNPGITATDVVLALTEFLRKERVVGAYLEFFGEGAKALTLGDRATISNMTPEYGATAAMFYIDE 309
                                       ***************************************************************************** PP

                         TIGR02333 309 qtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakev 385
                                       qtidyl+ltgr+e+qv+lve yak++glwad++  a y r+l+fdlssvvrn+agpsnpharlatsdlaakgia ++
  lcl|FitnessBrowser__SB2B:6939202 310 QTIDYLRLTGRDEKQVELVENYAKTTGLWADAMTGADYGRILTFDLSSVVRNMAGPSNPHARLATSDLAAKGIAADW 386
                                       ***************************************************************************** PP

                         TIGR02333 386 eeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkelek 462
                                       +ee+ g+mpdgaviiaaitsctntsnprnv+aagl+arna ++gl rkpwvk+slapgsk+v+lyl+eagll+ le+
  lcl|FitnessBrowser__SB2B:6939202 387 QEES-GKMPDGAVIIAAITSCTNTSNPRNVIAAGLIARNAVQKGLVRKPWVKTSLAPGSKAVELYLKEAGLLPYLEQ 462
                                       ***9.************************************************************************ PP

                         TIGR02333 463 lgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdi 539
                                       lgfgivafacttcngmsgaldpviqqeii+rdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagt+rfdi
  lcl|FitnessBrowser__SB2B:6939202 463 LGFGIVAFACTTCNGMSGALDPVIQQEIIERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTVRFDI 539
                                       ***************************************************************************** PP

                         TIGR02333 540 ekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdledaqkkvsplydwrpmstyirrppyweg 616
                                       ekdvlg+d  g+ + lkd+wp d+eida+++++vkpeqfr vy pmf+l  +  +  plydwrp+styirrppyweg
  lcl|FitnessBrowser__SB2B:6939202 540 EKDVLGIDDAGNAVTLKDLWPEDAEIDAIIKSSVKPEQFRAVYDPMFNLAVEYGTEKPLYDWRPQSTYIRRPPYWEG 616
                                       **************************************************8888899******************** PP

                         TIGR02333 617 alagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfn 693
                                       alagertl gmrplavlgdnittdhlspsnail++saageylakmglpeedfnsyathrgdhltaqratfanpklfn
  lcl|FitnessBrowser__SB2B:6939202 617 ALAGERTLSGMRPLAVLGDNITTDHLSPSNAILASSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFN 693
                                       ***************************************************************************** PP

                         TIGR02333 694 emvked.gkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegfer 769
                                       emvk+  gkvkqgslar+epegkv rmwe+ietym+rkqplii+ag dygqgssrdwaakgvrlagve ivaegfer
  lcl|FitnessBrowser__SB2B:6939202 694 EMVKDAdGKVKQGSLARLEPEGKVLRMWETIETYMERKQPLIIVAGKDYGQGSSRDWAAKGVRLAGVEVIVAEGFER 770
                                       ****866********************************************************************** PP

                         TIGR02333 770 ihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeag 846
                                       ihrtnlvgmgvlplef pg+ r t+++dgte++dv ge+tp+a+ltl+++r+nge++evpv crldtaeevs+yeag
  lcl|FitnessBrowser__SB2B:6939202 771 IHRTNLVGMGVLPLEFMPGETRMTYGIDGTETFDVKGERTPGAELTLLIRRQNGETVEVPVRCRLDTAEEVSIYEAG 847
                                       ***************************************************************************** PP

                         TIGR02333 847 gvlqrfaqdfle 858
                                       gvlqrfaqdfl+
  lcl|FitnessBrowser__SB2B:6939202 848 GVLQRFAQDFLA 859
                                       **********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (858 nodes)
Target sequences:                          1  (861 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: 00:00:00.06
# Mc/sec: 12.05
//
[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