Alignments for a candidate for acnD in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Desulfacinum infernum DSM 9756

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_073036524.1 BUB04_RS02125 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_900129305.1:WP_073036524.1
          Length = 881

 Score =  687 bits (1774), Expect = 0.0
 Identities = 382/879 (43%), Positives = 534/879 (60%), Gaps = 41/879 (4%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           M+ + R    G   ++ D    ++ +      +LPY+ RVL EN+VRR +  ++T    +
Sbjct: 1   MSARARLEKDGETFEFVD----LKGLFGNRLGRLPYSIRVLLENVVRRRDDRLVTERDVE 56

Query: 65  IIES-----KQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQ 119
            +        + ++ P+FPARV+  D  G  A+ DLA +RDA+ A G DPA VNP+VP  
Sbjct: 57  NLAGWRGRYAEPVEIPFFPARVLMQDFTGVPAVADLAAMRDALVALGKDPAAVNPLVPVD 116

Query: 120 LIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQI 179
           L+VDHS+ V++ G   DA   N   E  RN +R+ F+ W QK+F+N  V+P  +GI HQ+
Sbjct: 117 LVVDHSVQVDFFG-TSDALTANVRREYERNGERYTFLKWAQKSFENFRVVPPNSGICHQV 175

Query: 180 NLERMSPVIHARNG----VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASY 235
           NLE +S V   R      + FPDT+VG DSHT  V+ +GV+  GVGG+EAE+V++G+   
Sbjct: 176 NLEHLSRVFWDRKEDGVRICFPDTVVGLDSHTTMVNGIGVLGWGVGGIEAEAVLMGQPYS 235

Query: 236 MRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATI 295
           M +P++IGV L G+      ATD+VL +TE LR   VV  ++EFFG    AL++  RATI
Sbjct: 236 MAIPEVIGVRLVGRLPRRANATDLVLRVTEALRDYGVVEKFVEFFGPAVTALSVPARATI 295

Query: 296 SNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTL 355
           +NM+PE+GAT   F +D++ ++YL LT RE  Q ++ E  A+  GL+ D  ++  Y   L
Sbjct: 296 ANMSPEYGATVGFFPVDEKVVEYLRLTHRE-RQARVTEAAARAMGLYYDGSEEPDYTDVL 354

Query: 356 HFDLSSVVRTIAGPSNPHARVPTSELAAR------------GISGEVENEPGLMPDGAVI 403
             DLS++   +AGPS P  R+  SEL  R             +   +  E   + DG+V+
Sbjct: 355 EIDLSAIRPAVAGPSKPKDRIELSELKTRFRQLRGEDAPKAAVPVRIRGENVELSDGSVV 414

Query: 404 IAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPE 463
           IAAITSCTNTSNP  ++ A LLARNA  +GL     VKTSLAPGSK V  YL+ + LLP 
Sbjct: 415 IAAITSCTNTSNPHALLGAALLARNAVKRGLAVPAHVKTSLAPGSKVVVQYLDRSGLLPY 474

Query: 464 LESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAF 523
           LE+LGF  V F CTTC G SG L P +++ + + +L   AVLSGNRNF+ RIH   K  F
Sbjct: 475 LEALGFHPVAFGCTTCIGNSGPLHPEVERAIEEHNLNVAAVLSGNRNFEARIHQKVKSNF 534

Query: 524 LASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFR 583
           LASP LVVA+A+AG +  D+EK+ +GLD +G PV L +I P D EI+ ++   V+ + FR
Sbjct: 535 LASPLLVVAFALAGRVDVDLEKEPVGLDPNGGPVFLADILPDDEEIEELVNRYVQEDLFR 594

Query: 584 KVYEPMFDLSVDYGD---KVSPLYDWRPQSTYIRRPPYWEG---ALAGERTLKGMRPLAV 637
           + YE + +    + +   + S  Y W P+STYI+ PPY+EG    +     ++G R L  
Sbjct: 595 ETYEKILEGDQFWNELQVQESVTYPWDPRSTYIKCPPYFEGFTPQMPETTDIRGARVLLW 654

Query: 638 LGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLK 697
           LGD +TTDH+SP+ AI  D  AG YL  +GL  ++FNSY   RG+H    R TFAN +++
Sbjct: 655 LGDAVTTDHISPAGAIHEDYPAGRYLKSLGLSRQEFNSYGARRGNHEVMMRGTFANIRIR 714

Query: 698 NEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAK 757
           N++       + GS     PEG    ++EA E Y     PLI++ G +YG GSSRDWAAK
Sbjct: 715 NKLV-----SEPGSFTVKFPEGERMYVFEAAEAYRREGVPLIVLGGKEYGTGSSRDWAAK 769

Query: 758 GVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG--SIAP 815
           G +L GV+A++AE FERIHR+NL+GMG+LPL+F  GE+  + G+DGTE + + G   I P
Sbjct: 770 GPKLLGVKAVIAESFERIHRSNLIGMGILPLQFLEGESAESLGLDGTEEYHIAGIAGIEP 829

Query: 816 RADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
           R  LTV    K+G+     V  RLDT  E   Y  GG+L
Sbjct: 830 RRKLTVTAV-KDGKEKTFQVLARLDTEIEADYYRNGGIL 867


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: 1894
Number of extensions: 95
Number of successful extensions: 10
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: 881
Length adjustment: 42
Effective length of query: 825
Effective length of database: 839
Effective search space:   692175
Effective search space used:   692175
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 Apr 09 2024. 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)
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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 2024 update 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