Alignments for a candidate for acnD in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Dyella japonica UNC79MFTsu3.2

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate N515DRAFT_0029 N515DRAFT_0029 aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming)

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0029
          Length = 869

 Score = 1433 bits (3709), Expect = 0.0
 Identities = 713/865 (82%), Positives = 780/865 (90%), Gaps = 5/865 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MNT YR+ L GT+LDYFD R A+EAI PGAY  LPYTSRVLAENLVRRC+P +L  SLKQ
Sbjct: 1   MNTVYRQSLLGTSLDYFDARAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPAILAESLKQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           IIE K+E DFPWFPARVVCHDILGQTALVDLAGLRDAIA +GGDPA+VNPVVP QLIVDH
Sbjct: 61  IIERKRERDFPWFPARVVCHDILGQTALVDLAGLRDAIADRGGDPAKVNPVVPVQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE GGFD +AFA+NRAIEDRRNEDRFHFI WT++AF+N+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVECGGFDPNAFARNRAIEDRRNEDRFHFIEWTRQAFENVDVIPPGNGIMHQINLEKM 180

Query: 185 SPVIHARN-----GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLP 239
           SPVI  ++     GVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRAS+MRLP
Sbjct: 181 SPVIQVQHDDQGKGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP 240

Query: 240 DIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMT 299
           DIIGVELTGK QPGITATDIVLALTEFLR +KVV +YLEF GEGA +LTLGDRATISNM 
Sbjct: 241 DIIGVELTGKRQPGITATDIVLALTEFLRQEKVVGAYLEFRGEGAASLTLGDRATISNMA 300

Query: 300 PEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDL 359
           PE+GATAAMF+ID QTLDYL LTGR  EQV+LVETYAK AGLW+D L  A Y RTL FDL
Sbjct: 301 PEYGATAAMFFIDDQTLDYLRLTGRSDEQVRLVETYAKAAGLWADTLAAAQYERTLSFDL 360

Query: 360 SSVVRTIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNV 419
           SSVVR +AGPSNPH R+PT++LAARGI+G+ + +PG MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 SSVVRNMAGPSNPHKRLPTADLAARGIAGQWQEQPGQMPDGAVIIAAITSCTNTSNPRNV 420

Query: 420 IAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTC 479
           IAA LLARNANA+GL RKPWVK+SLAPGSKAV+LYL+EANLLPELE LGFGIV FACTTC
Sbjct: 421 IAAALLARNANARGLVRKPWVKSSLAPGSKAVELYLKEANLLPELEKLGFGIVAFACTTC 480

Query: 480 NGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 539
           NGMSGALDP IQQE+++RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 481 NGMSGALDPAIQQEIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540

Query: 540 RFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDK 599
           RFDIE+DVLG+D +G+PV L +IWPSD EID ++AASVKPEQFRKVYEPMF  +   G +
Sbjct: 541 RFDIEQDVLGIDANGQPVTLKDIWPSDEEIDTIVAASVKPEQFRKVYEPMFARTGRSGTR 600

Query: 600 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAA 659
            +PLYDWR QSTYIRRPPYWEGALAGERTLKGMR LAVLGDNITTDHLSPSNAIM DSAA
Sbjct: 601 AAPLYDWRAQSTYIRRPPYWEGALAGERTLKGMRALAVLGDNITTDHLSPSNAIMADSAA 660

Query: 660 GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEG 719
           GEYL +MGLPEEDFNSYATHRGDHLTAQRATFANP L NEMA+VDG+VK+GSLAR+EPEG
Sbjct: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLLNEMAVVDGEVKKGSLARVEPEG 720

Query: 720 IVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 779
            V RMWEAIETYM+RKQPLI+IAGADYGQGSSRDWAAKGVRLAGVEAI AEGFERIHRTN
Sbjct: 721 KVMRMWEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 780

Query: 780 LVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRL 839
           L+GMGVLPLEF+ G +R T GIDGTE FDV G+  PRA LT++I R+NGERVEVPVTCRL
Sbjct: 781 LIGMGVLPLEFQPGTDRKTLGIDGTETFDVTGARTPRAQLTLVIHRRNGERVEVPVTCRL 840

Query: 840 DTAEEVSIYEAGGVLQRFAQDFLES 864
           DTAEEVSIYEAGGVLQRFAQDFLE+
Sbjct: 841 DTAEEVSIYEAGGVLQRFAQDFLEA 865


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: 2255
Number of extensions: 92
Number of successful extensions: 2
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 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources