GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Pontibacillus litoralis JSM 072002

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_036833329.1 N784_RS06120 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000775615.1:WP_036833329.1
          Length = 904

 Score =  708 bits (1828), Expect = 0.0
 Identities = 389/896 (43%), Positives = 542/896 (60%), Gaps = 49/896 (5%)

Query: 13  LPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTAS-----LKQIIE 67
           L G   +Y+  +  +E    G  ++LPY+ RVL E+++R+ + E++         K   +
Sbjct: 15  LNGKKYNYYKLK-TLEEAGLGKISRLPYSIRVLLESVLRQHDGEVIQKEHIEKLAKWGSK 73

Query: 68  SKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLA 127
             + +D P+ P+RV+  D  G  A+VDLA LR A+   GG P ++NP VP  L++DHS+ 
Sbjct: 74  EAESVDVPFKPSRVILQDFTGVPAVVDLASLRKAMVDMGGSPDKINPEVPVDLVIDHSVQ 133

Query: 128 VEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPV 187
           V+  G  K A   N  +E  RN++R+ F+NW +KAF N   +P   GI+HQ+NLE ++ V
Sbjct: 134 VDEYGTAK-ALDANMELEFERNKERYEFLNWAKKAFDNYQAVPPATGIVHQVNLEYLANV 192

Query: 188 IHARNGV-----AFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDII 242
           +HA         A+PDTLVGTDSHT  ++ LGV+  GVGG+EAE+ MLG+ SY   P++I
Sbjct: 193 VHAIENEKGEYDAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAGMLGQPSYFPAPEVI 252

Query: 243 GVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEF 302
           GV+LTG    G TATD+ L +T+ LR + VV  ++EFFG G   + L DRATISNM PE+
Sbjct: 253 GVKLTGTLPKGTTATDLALKVTQKLREKNVVGKFVEFFGPGLTEMPLADRATISNMAPEY 312

Query: 303 GATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGL-WSDDLKQAVYPRTLHFDLSS 361
           GAT   F +DQ++L+YL LTGR  EQ++LVE Y K   L ++ D +   +   +   L  
Sbjct: 313 GATCGFFPVDQESLEYLRLTGRSEEQIQLVEAYCKENDLFYTPDQEDPTFTDLVEIKLDE 372

Query: 362 VVRTIAGPSNPHARVPTSEL---------AARGISG------------EVENEPG---LM 397
           +   ++GP  P   +P +E+         A  G  G             V++  G    M
Sbjct: 373 LEPNLSGPKRPQDLIPLTEMKESFNKALTAPEGNQGFGLDEKEKDKKVSVQHPSGKSSTM 432

Query: 398 PDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEE 457
             GAV IAAITSCTNTSNP  ++ AGLLA+ A  KGL    +VKTSLAPGSK V  YLE+
Sbjct: 433 KTGAVAIAAITSCTNTSNPYVMLGAGLLAKKAVEKGLEVPEYVKTSLAPGSKVVTRYLED 492

Query: 458 ANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHP 517
           + L+  LE LGF  VG+ CTTC G SG L P ++Q + D DL  ++VLSGNRNF+GRIHP
Sbjct: 493 SGLMTYLEKLGFNTVGYGCTTCIGNSGPLSPEVEQAIADNDLTVSSVLSGNRNFEGRIHP 552

Query: 518 YAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASV 577
             K  +LASPPLVVAYA+AGT+  D+ K+ LG D DGK V   +IWPS  EI A +   V
Sbjct: 553 LVKANYLASPPLVVAYALAGTVDIDLRKESLGKDHDGKDVHFDDIWPSMDEIKAEVDKHV 612

Query: 578 KPEQFRKVYEPMFDLSVDYGD---KVSPLYDWRPQSTYIRRPPYWEGAL---AGERTLKG 631
            PE FRK YE +FD +  +        PLY+W  +STYI+ PP++ G     +  + L G
Sbjct: 613 NPEIFRKEYEDVFDSNEKWNQIQTTDEPLYNWDDESTYIQNPPFFVGLSEDPSEVKDLDG 672

Query: 632 MRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATF 691
           +R +   GD++TTDH+SP+ AI  D  AG+YL   G+    FNSY + RG+H    R TF
Sbjct: 673 LRVIGKFGDSVTTDHISPAGAIAKDMPAGKYLQDKGVSPRHFNSYGSRRGNHEVMMRGTF 732

Query: 692 ANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSS 751
           AN +++N++A       +G      P   V  +++A   Y ++   L++IAG DYG GSS
Sbjct: 733 ANIRIRNKIA----PGTEGGYTTFWPTDEVMPIYDAAMKYQEQGTGLLVIAGNDYGMGSS 788

Query: 752 RDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFD--V 809
           RDWAAKG  L G++ ++AE FERIHR+NLV MGVLPL+FK G++  + G+ G E FD  +
Sbjct: 789 RDWAAKGTNLLGIKTVIAESFERIHRSNLVMMGVLPLQFKDGDSADSLGLSGKETFDIKI 848

Query: 810 IGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLESN 865
             ++ PR  + VI   + G + E  V  R D+  E+  Y  GG+LQ+  +D L+SN
Sbjct: 849 DETVKPRDLVDVIAIDEAGNKTEFQVIARFDSGVEIDYYRHGGILQKVLRDKLQSN 904


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: 1931
Number of extensions: 102
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: 904
Length adjustment: 43
Effective length of query: 824
Effective length of database: 861
Effective search space:   709464
Effective search space used:   709464
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