GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Erythrobacter marinus HWDM-33

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_047092295.1 AAV99_RS02180 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_001013305.1:WP_047092295.1
          Length = 890

 Score =  686 bits (1769), Expect = 0.0
 Identities = 381/887 (42%), Positives = 538/887 (60%), Gaps = 51/887 (5%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTAS--- 61
           + T+    + G +  Y+    A E    G  ++LP++ +VL EN++R  E E  T     
Sbjct: 9   LGTRKTLEVGGKSYAYYSLSAAEEKF--GDVSRLPHSMKVLLENMLR-FEDEGFTVGEEH 65

Query: 62  LKQIIESKQEL----DFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVP 117
           ++ I++ ++      +  + PARV+  D  G   +VDLA +RDAI   GGD A++NP VP
Sbjct: 66  VRAIVDWQKNPVTGNEIQYRPARVLLQDFTGVPCVVDLAAMRDAIGKLGGDTAKINPQVP 125

Query: 118 TQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMH 177
             L++DHS+ V+  G  K AF +N A+E  RN +R+ F+ W   + +N   +P G GI H
Sbjct: 126 VNLVIDHSVMVDEFGHPK-AFEQNMALEYERNAERYDFLKWGAVSLENFSAVPPGTGICH 184

Query: 178 QINLERMSPVIHA---RNG--VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGR 232
           Q+NLE +   + +   +NG  VA+PDT VGTDSHT  ++ LGV+  GVGG+EAE+ MLG+
Sbjct: 185 QVNLEHIGKGVWSSEDQNGELVAYPDTCVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 244

Query: 233 ASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDR 292
              M +P++ G  L GK   G+TATD+VL   + LR   VV  ++EF+G G   L+L DR
Sbjct: 245 PISMLIPEVAGFRLDGKMAEGVTATDLVLTCVQMLREHGVVGRFVEFYGPGVANLSLADR 304

Query: 293 ATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYP 352
           ATI+NM PE+GAT   F ID +TL+YL LTGR  E + LVE YAK  G+W     + V+ 
Sbjct: 305 ATIANMAPEYGATCGFFGIDDKTLEYLRLTGRPEETIALVEAYAKAQGMWFTPEAEPVFS 364

Query: 353 RTLHFDLSSVVRTIAGPSNPHARVPTSELAA------RGISGE-------VENEPGLMPD 399
            TL  D+++VV ++AGP  P  RV   E+        + + G+       VE +   + D
Sbjct: 365 STLQLDMATVVPSLAGPKRPQDRVALPEVDELFNSDLKKVYGKDAPARVRVEGKDHDVGD 424

Query: 400 GAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEAN 459
           G V+IAAITSCTNTSNP  +IAAGL+A+ A  KGL  KPWVKTSLAPGS+ V  YL ++ 
Sbjct: 425 GDVVIAAITSCTNTSNPDVLIAAGLVAKKAREKGLMPKPWVKTSLAPGSQVVTDYLVKSG 484

Query: 460 LLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYA 519
           L  +L+++GF +VG+ CTTC G SG L P I   + + DL A +VLSGNRNF+GR+ P  
Sbjct: 485 LQEDLDAIGFDLVGYGCTTCIGNSGPLAPPISAAINNNDLVAASVLSGNRNFEGRVSPDV 544

Query: 520 KQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKP 579
           +  FLASPPLVVAYA+ GT+  DI    +G D+DG  V L ++WPS+ EI    AA++  
Sbjct: 545 RANFLASPPLVVAYALKGTVTQDITTTPIGQDQDGNDVMLADLWPSNLEIAENRAANIDR 604

Query: 580 EQFRKVYEPMFD-------LSVDYGDKVSPLYDWRPQSTYIRRPPYWEGALAGERTLK-- 630
             F   Y  ++        + VD  D     Y+W P STY+  PPY++G       +K  
Sbjct: 605 SMFEARYADVYKGDEHWQAIKVDASD----TYNWNPASTYVANPPYFDGMSMEPDAIKDI 660

Query: 631 -GMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRA 689
            G +PLA+LGD++TTDH+SP+ +I  DS AG YL    +P++DFNSY + RG+H    R 
Sbjct: 661 EGAKPLAILGDSVTTDHISPAGSIKEDSPAGSYLVNHQVPKKDFNSYGSRRGNHEVMMRG 720

Query: 690 TFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQG 749
           TFAN ++KNEM  V G V+ G        G    +++A   +     PL++I G +YG G
Sbjct: 721 TFANIRIKNEM--VPG-VEGGETTY---NGEQMPIYDAAMKHKADGTPLVVIGGKEYGTG 774

Query: 750 SSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDV 809
           SSRDWAAKG  L GV A++ E +ERIHR+NL+GMGVLPL+F  G+ R + G+ G   F +
Sbjct: 775 SSRDWAAKGTILLGVRAVIVESYERIHRSNLIGMGVLPLQFNDGDTRNSLGLTGDCTFSI 834

Query: 810 --IGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
             +G ++P  D+ V +T+ +G  +     CR+DTA E+  Y  GG+L
Sbjct: 835 KGLGGLSPSQDVEVEVTKADGSTMSFMAKCRIDTANEMEYYRNGGIL 881


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: 1953
Number of extensions: 98
Number of successful extensions: 9
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 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