GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Lysobacter daejeonensis GH1-9

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_036138977.1 N800_RS12170 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000768355.1:WP_036138977.1
          Length = 869

 Score = 1427 bits (3694), Expect = 0.0
 Identities = 711/867 (82%), Positives = 781/867 (90%), Gaps = 7/867 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MN  +RKPLPGT LD+FD REA+EA+ PGA+A LPYT+RV AEN+VR+ +P M  A L+Q
Sbjct: 1   MNNAHRKPLPGTKLDWFDAREAVEALQPGAWATLPYTARVHAENIVRKADPAMRDAYLRQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           ++E +++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA KGGDPAQVNPVVP QLIVDH
Sbjct: 61  LVERRRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE GGFD DAFAKNRAIEDRRNEDRFHFI+WT++AF+N+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFRNVDVIPPGNGIMHQINLEKM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPVI+ ++GVAFPDT VGTDSHTPHVDALGVIA+GVGGLEAE+VMLGRAS+MRLPDI+GV
Sbjct: 181 SPVIYVQDGVAFPDTCVGTDSHTPHVDALGVIAVGVGGLEAENVMLGRASWMRLPDIVGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           ELTGKPQPGITATDIVL+LTEFLR QKVV +YLEF GEGA ALT+GDRATISNM PE+GA
Sbjct: 241 ELTGKPQPGITATDIVLSLTEFLRKQKVVGAYLEFRGEGAAALTIGDRATISNMAPEYGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TAAMF+ID  TLDYL LTGR  EQV LVETYAK AGLW+DDL+ A Y RTLHFDLSSV R
Sbjct: 301 TAAMFFIDDNTLDYLRLTGRSDEQVALVETYAKAAGLWADDLRTAQYERTLHFDLSSVER 360

Query: 365 TIAGPSNPHARVPTSELAARGISGEVE-----NEPGLMPDGAVIIAAITSCTNTSNPRNV 419
           T+AGPSNPHAR+P ++LA RGI+G +E        GL+PDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 TMAGPSNPHARLPVAQLAERGIAGNLEAARAQEAQGLLPDGAVIIAAITSCTNTSNPRNV 420

Query: 420 IAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTC 479
           IAAGLLARNA   GL RKPWVKTSLAPGSKAV LYL+EA L  +LE LGFGIV FACTTC
Sbjct: 421 IAAGLLARNAARLGLQRKPWVKTSLAPGSKAVALYLDEAGLTDDLEQLGFGIVAFACTTC 480

Query: 480 NGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 539
           NGMSGALDP IQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540

Query: 540 RFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDK 599
           RFDIEKDVLG+  DG+ +RL ++WP+DAEIDAV+ A+VKPEQFRKVYEPMF++ V++G  
Sbjct: 541 RFDIEKDVLGV-VDGREIRLKDLWPTDAEIDAVMKAAVKPEQFRKVYEPMFNVRVEHGGA 599

Query: 600 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAA 659
           VSPLYDWRPQSTYIRRPPYWEGALAGERTL+GMRPLAVLGDNITTDHLSPSNAI++DSAA
Sbjct: 600 VSPLYDWRPQSTYIRRPPYWEGALAGERTLRGMRPLAVLGDNITTDHLSPSNAILLDSAA 659

Query: 660 GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIV-DGKVKQGSLARIEPE 718
           GEYL KMGLPEEDFNSYATHRGDHLTAQRATFANPKL NEM    DG V+QGSLARIEPE
Sbjct: 660 GEYLDKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRKDDGSVRQGSLARIEPE 719

Query: 719 GIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 778
           G VTRMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT
Sbjct: 720 GQVTRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 779

Query: 779 NLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCR 838
           NL+GMGVLPLEF+ G +R T  IDGTE +DVIG   PRA LT++I R+NGERVEVPVTCR
Sbjct: 780 NLIGMGVLPLEFQPGADRTTLAIDGTETYDVIGERTPRATLTLVIHRRNGERVEVPVTCR 839

Query: 839 LDTAEEVSIYEAGGVLQRFAQDFLESN 865
           LDTAEEVSIYEAGGVLQRFA DFLES+
Sbjct: 840 LDTAEEVSIYEAGGVLQRFANDFLESS 866


Lambda     K      H
   0.318    0.136    0.397 

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: 2271
Number of extensions: 97
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: 867
Length of database: 869
Length adjustment: 42
Effective length of query: 825
Effective length of database: 827
Effective search space:   682275
Effective search space used:   682275
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)

This GapMind analysis is from Sep 24 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