Alignments for a candidate for acnD in Halomonas stevensii S18214

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Halomonas stevensii S18214

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_016914362.1 HSS18214_RS0105820 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000275725.1:WP_016914362.1
          Length = 880

 Score = 1363 bits (3529), Expect = 0.0
 Identities = 681/877 (77%), Positives = 759/877 (86%), Gaps = 16/877 (1%)

Query: 5   MNTQYRKPLP-----GTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLT 59
           MNT YRKPLP     G  +D+FDTR+A+E I PGAYA+LPYTSRVLAE LVRRC+P +LT
Sbjct: 1   MNTNYRKPLPNVSVAGAPVDFFDTRQAVEEIQPGAYAQLPYTSRVLAEQLVRRCDPALLT 60

Query: 60  ASLKQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQ 119
            +LKQ+IE KQELDFPW+PARVVCHDILGQTALVDLAGLRDAIA KGGDPA+VNPVVPTQ
Sbjct: 61  DALKQLIERKQELDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPAKVNPVVPTQ 120

Query: 120 LIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQI 179
           LIVDHSLAVE+ GF+KDAF KNR +EDRRN+DRFHFINWT+ AF+N+DVIP GNGIMHQI
Sbjct: 121 LIVDHSLAVEHAGFEKDAFEKNRQVEDRRNDDRFHFINWTKLAFENVDVIPPGNGIMHQI 180

Query: 180 NLERMSPVIHARNG-----VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRAS 234
           NLE+MSPV+  R       VA+PDT VGTDSHTP VDALGVI++GVGGLEAESVMLGRAS
Sbjct: 181 NLEKMSPVVQCRPDEQGVQVAYPDTCVGTDSHTPMVDALGVISVGVGGLEAESVMLGRAS 240

Query: 235 YMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRAT 294
            MRLPDI+GVELTGK QPGIT TD+VLA+TEFLR ++VV +YLEFFGEGA+AL++GDRAT
Sbjct: 241 MMRLPDIVGVELTGKLQPGITGTDMVLAITEFLRRERVVGAYLEFFGEGADALSVGDRAT 300

Query: 295 ISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRT 354
           ISNMTPE+GATAAMFYID QT+DYL LTGR+ EQV LV+ YA+  GLW+DDL Q VY R 
Sbjct: 301 ISNMTPEYGATAAMFYIDDQTIDYLKLTGRDDEQVALVKAYAQHTGLWADDLTQVVYERI 360

Query: 355 LHFDLSSVVRTIAGPSNPHARVPTSELAARGIS-----GEVENEPGLMPDGAVIIAAITS 409
           L FDLSSV RT+AGPSNPHA +PT+ELA RGI+        E   G MPDGAVIIAAITS
Sbjct: 361 LRFDLSSVTRTLAGPSNPHAHLPTTELAKRGIAVGLDKAREEEAAGKMPDGAVIIAAITS 420

Query: 410 CTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGF 469
           CTNTSNPRN++AAGL+ARNAN  GLTRKPWVKTSLAPGSK V++YLEEA L+ ELE+LGF
Sbjct: 421 CTNTSNPRNMVAAGLIARNANRLGLTRKPWVKTSLAPGSKTVKMYLEEAELMGELEALGF 480

Query: 470 GIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPL 529
           G+V +ACTTCNGMSGAL+P IQ+E+I RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPL
Sbjct: 481 GVVAYACTTCNGMSGALEPSIQEEIIRRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPL 540

Query: 530 VVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPM 589
           VVAYAIAGTIRFDIE+DVLG D  G PV L +IWP D+EIDA++ ASVKPEQFR+ Y PM
Sbjct: 541 VVAYAIAGTIRFDIEQDVLGHDAQGNPVTLKDIWPEDSEIDAIVKASVKPEQFRETYIPM 600

Query: 590 FDLSVDYGDKVSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSP 649
           FDL    G +VSPLY+WRPQSTYIRRPPYWEG +A ER LKGMRPLA+L DNITTDHLSP
Sbjct: 601 FDLDKRAGPQVSPLYEWRPQSTYIRRPPYWEGNMARERGLKGMRPLAILPDNITTDHLSP 660

Query: 650 SNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVD-GKVK 708
           SNAI+MDSAAGEYLH MGLPEEDFNSYATHRGDHLTAQRAT ANPKL NEM   + GKV 
Sbjct: 661 SNAILMDSAAGEYLHAMGLPEEDFNSYATHRGDHLTAQRATLANPKLFNEMVHDEQGKVM 720

Query: 709 QGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIV 768
           QGSLARIEPEG VTRMWEAIETYM RKQPLIIIAGADYGQGSSRDWAAKGV LAGVEAIV
Sbjct: 721 QGSLARIEPEGTVTRMWEAIETYMARKQPLIIIAGADYGQGSSRDWAAKGVALAGVEAIV 780

Query: 769 AEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNG 828
           AEGFERIHRTNLVGMGV+PL+F+ G  R T  +DGTE++DV G+ APRA LT++I R+ G
Sbjct: 781 AEGFERIHRTNLVGMGVMPLQFEEGTTRKTLALDGTEIYDVEGTPAPRAQLTLVIHRQQG 840

Query: 829 ERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLESN 865
               VPV CRLDTAEEV+IY AGGVLQRFAQDFLES+
Sbjct: 841 AVERVPVVCRLDTAEEVTIYSAGGVLQRFAQDFLESS 877


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: 2216
Number of extensions: 102
Number of successful extensions: 5
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: 880
Length adjustment: 42
Effective length of query: 825
Effective length of database: 838
Effective search space:   691350
Effective search space used:   691350
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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