Alignments for a candidate for acn in Nocardiopsis lucentensis DSM 44048

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Nocardiopsis lucentensis DSM 44048

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_017598314.1 D471_RS0108975 aconitate hydratase AcnA

Query= SwissProt::O53166
         (943 letters)



>NCBI__GCF_000341125.1:WP_017598314.1
          Length = 904

 Score = 1397 bits (3617), Expect = 0.0
 Identities = 684/936 (73%), Positives = 784/936 (83%), Gaps = 35/936 (3%)

Query: 5   SVNSFGAHDTLKVGEKSYQIYRLDAVPNTAKLPYSLKVLAENLLRNEDGSNITKDHIEAI 64
           S NSFGA DTL+VG++SY+I+RLDAV    +LPYSLKVL ENLLR EDG+N+T DHI A+
Sbjct: 2   SANSFGARDTLRVGDESYEIFRLDAVQGANRLPYSLKVLLENLLRTEDGANVTADHIRAL 61

Query: 65  ANWDPKAEPSIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAPADLV 124
             WD KA+PS EIQ+TPARV+MQDFTGVPC+VDLATMREA+ DLGG+PDK+NPLAPA+LV
Sbjct: 62  GEWDAKAQPSQEIQFTPARVIMQDFTGVPCVVDLATMREAVRDLGGDPDKINPLAPAELV 121

Query: 125 IDHSVIADLFGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTGIVHQVNIE 184
           IDHSV+ DLFGR DAFERNVEIEY+RN ERY+FLRWGQ AFD+FKVVPPGTGIVHQ NIE
Sbjct: 122 IDHSVVVDLFGRPDAFERNVEIEYERNYERYKFLRWGQTAFDEFKVVPPGTGIVHQANIE 181

Query: 185 YLASVVMTRDGVAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSMLIPRVV 244
           +LA V M+R+G AYPDTCVGTDSHTTM NGLG+LGWGVGGIEAEAAMLGQP+SMLIPRVV
Sbjct: 182 HLARVTMSRNGQAYPDTCVGTDSHTTMQNGLGILGWGVGGIEAEAAMLGQPISMLIPRVV 241

Query: 245 GFRLTGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRATLGNMSPEF 304
           GF+L+G+++PG TATD+VLT+TE LR+HGVVGKFVEFYGEGV+ VPLANRAT+GNMSPEF
Sbjct: 242 GFKLSGQLKPGTTATDLVLTITEKLREHGVVGKFVEFYGEGVSSVPLANRATIGNMSPEF 301

Query: 305 GSTAAIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDPKHEPEFSEYLELNLSDV 364
           GSTAAIFP+D+ETI+Y+R TGR+ +QVAL EAYAKA G WHDP  EPE+SEYLEL+L++V
Sbjct: 302 GSTAAIFPVDDETIRYMRLTGRSEQQVALTEAYAKANGFWHDPAVEPEYSEYLELDLAEV 361

Query: 365 VPSIAGPKRPQDRIALAQAKSTFREQIYHYVGNGSPDSPHDPHSKLDEVVEETFPASDPG 424
           VPSIAGPKRPQDRIAL++AK T+R  +++YV +             DE  EE+FPASD  
Sbjct: 362 VPSIAGPKRPQDRIALSEAKPTWRHDVHNYVSD-------------DEAGEESFPASD-- 406

Query: 425 QLTFANDDVATDETVHSAAAHADGRVSNPVRVKSDELGEFVLDHGAVVIAAITSCTNTSN 484
                           + A  A+GR   PV+V   +  E  +DHGAVVIAAITSCTNTSN
Sbjct: 407 ----------------APATTANGRPHRPVKVTMADGTETEVDHGAVVIAAITSCTNTSN 450

Query: 485 PEVMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLEKLGFYLVGYG 544
           P VMLGAALLA+ AVEKGL+ KPWVKT++APGS+VV DYY+RSGL PYL+KLGF LVGYG
Sbjct: 451 PSVMLGAALLAKKAVEKGLSRKPWVKTSMAPGSKVVTDYYERSGLTPYLDKLGFNLVGYG 510

Query: 545 CTTCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYLASPPLVIAYAL 604
           CTTCIGNSGPLPEEISKAV DNDL+VTAVLSGNRNFEGRINPDVKMNYLASPPLV+AYAL
Sbjct: 511 CTTCIGNSGPLPEEISKAVQDNDLAVTAVLSGNRNFEGRINPDVKMNYLASPPLVVAYAL 570

Query: 605 AGTMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTRNYADVFKGDDR 664
           AG++D D  T+PLG   DGK V+L DIWPS +++ + + AAI  +M+   YADVF GD+R
Sbjct: 571 AGSLDVDITTEPLGVGSDGKPVYLADIWPSAEEIQEVMDAAIASDMYESAYADVFAGDER 630

Query: 665 WRNLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALLGDSVTTDHISP 724
           WR+LPTP+GNTFEW+  STYVRKPPYFEGM   P  V +I+GARVLA LGDSVTTDHISP
Sbjct: 631 WRSLPTPTGNTFEWEDESTYVRKPPYFEGMATTPSAVTDITGARVLAKLGDSVTTDHISP 690

Query: 725 AGAIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRNQLLDDVSGGYT 784
           AGAIKPGTPAA YL  HGV+R+D+NS+GSRRGNHEVMIRGTFANIRLRNQ+     GGYT
Sbjct: 691 AGAIKPGTPAAEYLKSHGVERRDFNSYGSRRGNHEVMIRGTFANIRLRNQIAPGTEGGYT 750

Query: 785 RDFTQPGGPQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTLLLGVRAVIAES 844
           RDFTQP  P +FIYDAAQNYAAQ IPLVV GGKEYGSGSSRDWAAKGT LLGVRAVI ES
Sbjct: 751 RDFTQPEAPVSFIYDAAQNYAAQDIPLVVLGGKEYGSGSSRDWAAKGTRLLGVRAVITES 810

Query: 845 FERIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKTPKTVCVQATKG 904
           +ERIHRSNLIGMGV+PLQFPEG+SA SLGL G E F ITG+  LN+G+ P TV V    G
Sbjct: 811 YERIHRSNLIGMGVLPLQFPEGQSADSLGLTGEETFSITGVTELNEGRVPSTVKVSTDTG 870

Query: 905 DGATIEFDAVVRIDTPGEADYYRNGGILQYVLRNIL 940
               +EFDAVVRIDTPGEADYYRNGGILQYVLR ++
Sbjct: 871 ----VEFDAVVRIDTPGEADYYRNGGILQYVLRQLI 902


Lambda     K      H
   0.316    0.136    0.403 

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: 2557
Number of extensions: 115
Number of successful extensions: 4
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: 943
Length of database: 904
Length adjustment: 43
Effective length of query: 900
Effective length of database: 861
Effective search space:   774900
Effective search space used:   774900
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 (21.6 bits)
S2: 57 (26.6 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