Alignments for a candidate for acnD in Actinomyces timonensis 7400942

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Actinomyces timonensis 7400942

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_017178478.1 A1QA_RS0108460 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000295095.1:WP_017178478.1
          Length = 890

 Score =  700 bits (1806), Expect = 0.0
 Identities = 389/891 (43%), Positives = 541/891 (60%), Gaps = 62/891 (6%)

Query: 16  TALDYFDTREAIEA-----------IAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           T++D F +R  ++             APG   +LPY+ +VLAENL+R  +   +TA   +
Sbjct: 2   TSIDTFGSRATLDVDGAAYEYYRLNAAPGL-ERLPYSLKVLAENLLRTEDGANVTADHVR 60

Query: 65  IIES-----KQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQ 119
            + +     + + +  + PARVV  D  G   +VDLA +R+A+A  GGDP  +NP+ P +
Sbjct: 61  ALAAWDPAAEPDTEIQFTPARVVMQDFTGVPCIVDLATMREAVAELGGDPEVINPLAPAE 120

Query: 120 LIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQI 179
           +++DHS+ ++  G    +  +N+  E  RN +R+ F+ W Q A  N  V+P G GI+HQ+
Sbjct: 121 MVIDHSVQIDSFGLP-GSLERNKEREYERNAERYQFLRWGQGALSNFRVVPPGTGIVHQV 179

Query: 180 NLERMSPVI--HARNGV--AFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASY 235
           N+E ++ ++  H  +GV  A+PDT VGTDSHT  V+ LGV+  GVGG+EAE+ MLG+   
Sbjct: 180 NIEYLARIVFTHEADGVTRAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVS 239

Query: 236 MRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATI 295
           M +P ++G +L+G    G TATD+VL +TE LRA  VV  ++EF+GEG   + L +RATI
Sbjct: 240 MLIPKVVGFKLSGAIPAGATATDVVLTITEMLRAHGVVGKFVEFYGEGVAEVPLANRATI 299

Query: 296 SNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTL 355
            NM+PEFG+TAA+F ID+ TLDYL LTGR  E+V+LVE Y K  G+W D  ++ VY   L
Sbjct: 300 GNMSPEFGSTAAIFPIDEITLDYLRLTGRSEERVRLVEAYTKAQGMWHDPAREPVYSEYL 359

Query: 356 HFDLSSVVRTIAGPSNPHARVPTS-------ELAARGISGEVENEPGLMPDGA------- 401
             DLS+VV +IAGP  P  R+  S       E+     S   +  P  + DG        
Sbjct: 360 ELDLSTVVPSIAGPKRPQDRIVLSRAKESFQEVLPTYASQPSKPTPVTLADGTATDLDHG 419

Query: 402 -VIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANL 460
            V IA+ITSCTNTSNP  ++AAGLLARNA A+GL  KPWVKTS APGS+ V  Y E+A L
Sbjct: 420 HVAIASITSCTNTSNPSVMMAAGLLARNAVARGLRSKPWVKTSTAPGSQVVTDYYEKAGL 479

Query: 461 LPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAK 520
            P L  LGF +VG+ C TC G SG L   + Q V D DL   +VLSGNRNF+GRI+P  K
Sbjct: 480 WPALNELGFNVVGYGCATCIGNSGPLPAEVSQAVNDADLAVVSVLSGNRNFEGRINPDVK 539

Query: 521 QAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPE 580
             +LASPPLV+AYA+AGT+  D   + LG D +G+ V L +IWP   E+ AVI +++  E
Sbjct: 540 MNYLASPPLVIAYALAGTMDIDFATEPLGQDPEGRDVFLSDIWPDPTEVQAVIDSTIDRE 599

Query: 581 QFRKVYEPMF-------DLSVDYGDKVSPLYDWRPQSTYIRRPPYWEG---ALAGERTLK 630
            + + Y  +F        L    GD     + W   STY+R+ P++EG    L     ++
Sbjct: 600 MYTRDYADVFAGDERWQGLDTPEGD----TFAWDKDSTYVRKAPFFEGLSMELTPVADIE 655

Query: 631 GMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRAT 690
             R LA+LGD++TTDH+SP+ AI  DS AG YL + G+   DFNSY + RG+H    R T
Sbjct: 656 DARVLALLGDSVTTDHISPAGAIKADSPAGRYLAEHGVARADFNSYGSRRGNHEVMIRGT 715

Query: 691 FANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGS 750
           FAN +L+N   ++DG   +G   R    G    +++A + Y     PL+++ G +YG GS
Sbjct: 716 FANIRLRNR--LLDG--VEGGYTRNFLTGEQESIFDASQAYQAAGIPLVVLGGKEYGSGS 771

Query: 751 SRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVI 810
           SRDWAAKG  L GV+A++AE FERIHR+NL+GMGV+PL+F AGE+  + G+DGTE F + 
Sbjct: 772 SRDWAAKGTALLGVKAVIAESFERIHRSNLIGMGVVPLQFPAGESAESLGLDGTETFSIT 831

Query: 811 GSIA------PRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQ 855
           G  A      PR  + V   + +G  V      R+DT  E   +  GG+LQ
Sbjct: 832 GLTALNEGTTPRT-VAVTAQKADGSAVSFDAVVRIDTPGEADYFRHGGILQ 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: 1978
Number of extensions: 78
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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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 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