Alignments for a candidate for acn in Nocardioides dokdonensis FR1436

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Nocardioides dokdonensis FR1436

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_068112647.1 I601_RS17670 aconitate hydratase

Query= SwissProt::O53166
         (943 letters)



>NCBI__GCF_001653335.1:WP_068112647.1
          Length = 936

 Score = 1313 bits (3397), Expect = 0.0
 Identities = 658/946 (69%), Positives = 767/946 (81%), Gaps = 22/946 (2%)

Query: 5   SVNSFGAHDTLKVGEKSYQIYRLDAVP----NTAKLPYSLKVLAENLLRNEDGSNITKDH 60
           S +SFGA  TL V   SY+I+RLDAV     + A LP+SLKVL ENLLR EDGS+IT D 
Sbjct: 3   SKDSFGAKGTLDVDGTSYEIFRLDAVSGDGLDVASLPFSLKVLLENLLRTEDGSDITADD 62

Query: 61  IEAIANWDPKAEPSIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAP 120
           ++AIA WD  A+PS EIQ+TPARV+MQDFTGVPC+VDLATMREA+ADLGG+P K+NPLAP
Sbjct: 63  VKAIAGWDADADPSQEIQFTPARVIMQDFTGVPCVVDLATMREAMADLGGDPTKINPLAP 122

Query: 121 ADLVIDHSVIADLFGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTGIVHQ 180
           A++VIDHSVIAD+FG  +AF RNVEIEY+RN ERYQFLRWGQGAFDDFKVVPPGTGIVHQ
Sbjct: 123 AEMVIDHSVIADVFGTPEAFGRNVEIEYERNRERYQFLRWGQGAFDDFKVVPPGTGIVHQ 182

Query: 181 VNIEYLASVVMTR--DGV--AYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPV 236
           VNIE+LA  V TR  DGV  AYPDTCVGTDSHTTMVNG+GV+GWGVGGIEAEAAMLGQPV
Sbjct: 183 VNIEHLARTVFTREVDGVLQAYPDTCVGTDSHTTMVNGIGVVGWGVGGIEAEAAMLGQPV 242

Query: 237 SMLIPRVVGFRLTGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRAT 296
           SMLIPRVVGF+L G++  G TATD+VLT+TEMLR+HGVVGKFVEFYG GV+ +PLANRAT
Sbjct: 243 SMLIPRVVGFKLNGDLPEGATATDLVLTITEMLREHGVVGKFVEFYGPGVSVLPLANRAT 302

Query: 297 LGNMSPEFGSTAAIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDPKHEPEFSEY 356
           +GNMSPEFGST A+FPIDEET KYL  TGRTPEQ+ALVEAYAK QG+WHDP  EP FSE 
Sbjct: 303 IGNMSPEFGSTIAVFPIDEETTKYLELTGRTPEQIALVEAYAKEQGLWHDPDAEPRFSEK 362

Query: 357 LELNLSDVVPSIAGPKRPQDRIALAQAKSTFREQIYHYVGNGSPDSPHDPHSKLDEVVEE 416
           LEL+L+ VVPS+AGPKRPQDR++L++AK +FR  +  Y    + D+        DE VEE
Sbjct: 363 LELDLATVVPSLAGPKRPQDRVSLSEAKESFRSALADY----AEDTDAQETKGYDENVEE 418

Query: 417 TFPASDPGQLTFANDDVATDETVHSAAAH-ADGRVSNPVRVKSDELGEFVLDHGAVVIAA 475
           +FPASD    T  N         H AA   A GR  NP +V   +   F LDHGAV IAA
Sbjct: 419 SFPASD----TPHNGHGEAPPNGHVAAGSGAGGRPRNPAQVTLADGTSFELDHGAVTIAA 474

Query: 476 ITSCTNTSNPEVMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLEK 535
           ITSCTNTSNP VM+GAALLA+ AVEKGL  KPWVKTT+APGS+VV+DYY++SGL PYL+K
Sbjct: 475 ITSCTNTSNPSVMIGAALLAKKAVEKGLERKPWVKTTLAPGSKVVSDYYEKSGLTPYLDK 534

Query: 536 LGFYLVGYGCTTCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYLAS 595
           LGF LVGYGCTTCIGNSGPL  E+S+AVNDNDL+V +VLSGNRNFEGRINPDVKMNYLAS
Sbjct: 535 LGFNLVGYGCTTCIGNSGPLIPEVSQAVNDNDLAVVSVLSGNRNFEGRINPDVKMNYLAS 594

Query: 596 PPLVIAYALAGTMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTRNY 655
           PPLV+AYALAG+MD D    PLGQD +G +V+++DIWP+  ++ + +A+AI  +MF   Y
Sbjct: 595 PPLVVAYALAGSMDVDLFNDPLGQDTEGNDVYMKDIWPTSAEIEEVVASAITSDMFDDGY 654

Query: 656 ADVFKGDDRWRNLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALLGD 715
           ADVF GD++WR+LPTP G TFEWD  STYVRKPPYF+GM  +PEPV +I GARVL  LGD
Sbjct: 655 ADVFAGDEQWRSLPTPEGKTFEWDAESTYVRKPPYFDGMPQEPEPVTDIDGARVLLKLGD 714

Query: 716 SVTTDHISPAGAIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRNQL 775
           SVTTDHISPAGAIK  +PA  YL EHGV+++D+NS+GSRRGNHEVMIRGTFANIRLRNQ+
Sbjct: 715 SVTTDHISPAGAIKKDSPAGHYLAEHGVEQRDFNSYGSRRGNHEVMIRGTFANIRLRNQM 774

Query: 776 LDDVSGGYTRDFTQPGGPQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTLLL 835
                GG+TR           +++A++ Y A  +PLVV  GKEYGSGSSRDWAAKGT LL
Sbjct: 775 APGTEGGFTRYLDGGEDSVTSVFEASEKYIAAGVPLVVLAGKEYGSGSSRDWAAKGTALL 834

Query: 836 GVRAVIAESFERIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKTPK 895
           GV+AVIAES+ERIHRSNLIGMGV+PLQ+PEG+SA SLGL G E F ++G+  LNDG TP+
Sbjct: 835 GVKAVIAESYERIHRSNLIGMGVLPLQYPEGESAESLGLTGEETFSVSGVTELNDGTTPR 894

Query: 896 TVCVQATKGDGATIEFDAVVRIDTPGEADYYRNGGILQYVLRNILK 941
           TV V A   DG  +EFDAVVRIDTPGEA+YYRNGGI+QYVLRN+L+
Sbjct: 895 TVKVTA---DG--VEFDAVVRIDTPGEANYYRNGGIMQYVLRNLLR 935


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: 2663
Number of extensions: 128
Number of successful extensions: 7
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: 936
Length adjustment: 44
Effective length of query: 899
Effective length of database: 892
Effective search space:   801908
Effective search space used:   801908
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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 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