Alignments for a candidate for acnD in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Sphingomonas koreensis DSMZ 15582

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate Ga0059261_3296 Ga0059261_3296 aconitate hydratase 1

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Korea:Ga0059261_3296
          Length = 890

 Score =  700 bits (1806), Expect = 0.0
 Identities = 392/885 (44%), Positives = 543/885 (61%), Gaps = 45/885 (5%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           + T+    + G +  Y+   +A   +  G  ++LP++ +VL EN++R  +   +T    Q
Sbjct: 9   LGTRETLTVGGKSYSYYSLEKAAAKL--GDVSRLPFSMKVLLENMLRFEDGVTVTPEDAQ 66

Query: 65  IIESKQ------ELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPT 118
            I   Q      E +  + PARV+  D  G   +VDLA +RDAI   GGD A++NP VP 
Sbjct: 67  AIVDWQKNPNAPEREIQYRPARVLMQDFTGVPCVVDLAAMRDAITKLGGDAAKINPQVPV 126

Query: 119 QLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQ 178
            L++DHS+ V+  G  K AF +N  +E +RN +R+ F+ W  K+  N  V+P G GI HQ
Sbjct: 127 HLVIDHSVMVDEFGTPK-AFEENVELEYQRNMERYDFLKWGSKSLDNFKVVPPGTGICHQ 185

Query: 179 INLERMSPVIHARNG-----VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRA 233
           +NLE ++  I +        VA+PDTLVGTDSHT  V+ LGV+  GVGG+EAE+ MLG+ 
Sbjct: 186 VNLEYIADAIWSSTAADGTTVAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQP 245

Query: 234 SYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRA 293
             M +P+++G +LTGK Q GITATD+VL +T+ LRA+ VV  ++EFFG G   +TL DRA
Sbjct: 246 VSMLIPEVVGFKLTGKLQEGITATDLVLTVTQMLRARGVVGRFVEFFGPGLATMTLADRA 305

Query: 294 TISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWS-DDLKQAVYP 352
           TI+NM PE+GAT   F ID +TLDY+ LTGR+ + V LVE Y K  G+W  DD+   ++ 
Sbjct: 306 TIANMAPEYGATCGFFGIDDKTLDYMRLTGRDDDTVTLVEAYCKAQGMWRYDDMADPIFT 365

Query: 353 RTLHFDLSSVVRTIAGPSNPHARVPTSEL-------------AARGISGEVENEPGLMPD 399
            TL  D+++V  ++AGP  P  RV  +++                G    VE +   + D
Sbjct: 366 DTLELDMATVTASLAGPKRPQDRVSLNKVDEVFNGDLFKVYGKENGHRVAVEGKDHDIGD 425

Query: 400 GAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEAN 459
           G V+IAAITSCTNTSNP  +IAAGL+AR A AKGLTRKPWVKTSLAPGS+ V  YL +A 
Sbjct: 426 GDVVIAAITSCTNTSNPSVLIAAGLVARKARAKGLTRKPWVKTSLAPGSQVVTDYLNKAG 485

Query: 460 LLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYA 519
           L  +L+++GF +VG+ CTTC G SG L   I   +   D+ A +VLSGNRNF+GR+ P  
Sbjct: 486 LSEDLDAIGFNLVGYGCTTCIGNSGPLAQPISDAINGNDIVAASVLSGNRNFEGRVSPDV 545

Query: 520 KQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKP 579
           +  FLASPPLVVAYA+ GT+  D+ +  +G   DG PV L +IWP++ E+  VI A++  
Sbjct: 546 RANFLASPPLVVAYALKGTVTEDMIETPIGEGTDG-PVYLKDIWPTNEEVQGVINANIDS 604

Query: 580 EQFRKVYEPMFDLSVDYGDKV----SPLYDWRPQSTYIRRPPYWEGAL---AGERTLKGM 632
           E F+  Y  ++ L   +  K+    S  Y W   STYI  PPY+ G     A    +   
Sbjct: 605 EMFKSRYGNVY-LGDAHWQKINVEGSATYSWPAASTYIANPPYFAGMTMTPAPVADIVDA 663

Query: 633 RPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFA 692
           +PLA+LGD+ITTDH+SP+ +I  DS AG++L +  + + DFNSY   RG+     R TFA
Sbjct: 664 KPLAILGDSITTDHISPAGSIKADSPAGKWLMERQVSKADFNSYGARRGNDNVMVRGTFA 723

Query: 693 NPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSR 752
           N +++NEM  V G V+ G  +     G    +++A   +     PL+I+AG +YG GSSR
Sbjct: 724 NIRIRNEM--VPG-VEGGMTSY---AGETMPIYDAAMRHKADGTPLVIVAGKEYGTGSSR 777

Query: 753 DWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG- 811
           DWAAKG  L GV A++ E FERIHR+NLVGMGVLPL+F  G  R T  +DG+E F + G 
Sbjct: 778 DWAAKGTNLLGVRAVITESFERIHRSNLVGMGVLPLQFAEGVTRQTLKLDGSETFTITGV 837

Query: 812 -SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQ 855
             + PR D+ V +TR +G        CR+DT  E+  +  GG+LQ
Sbjct: 838 AGLRPRQDVEVKLTRADGSSETFLTRCRIDTVNELEYFLNGGILQ 882


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: 1946
Number of extensions: 105
Number of successful extensions: 12
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: 890
Length adjustment: 43
Effective length of query: 824
Effective length of database: 847
Effective search space:   697928
Effective search space used:   697928
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