Alignments for a candidate for acn in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudarthrobacter sulfonivorans Ar51

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_058929322.1 AU252_RS02190 aconitate hydratase AcnA

Query= SwissProt::O53166
         (943 letters)



>NCBI__GCF_001484605.1:WP_058929322.1
          Length = 936

 Score = 1365 bits (3533), Expect = 0.0
 Identities = 676/941 (71%), Positives = 780/941 (82%), Gaps = 16/941 (1%)

Query: 5   SVNSFGAHDTLKVGEKSYQIYRLDAVPNTAKLPYSLKVLAENLLRNEDGSNITKDHIEAI 64
           +V+SFG+   L V    Y+I+RL++V     LP+SLKVL ENLLR EDG+NIT DH+ A+
Sbjct: 3   TVDSFGSKGKLNVAGTEYEIFRLNSVEGAENLPFSLKVLLENLLRTEDGANITADHVRAL 62

Query: 65  ANWDPKAEPSIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAPADLV 124
           A WDP A+P+ EIQ+TPARV+MQDFTGVPC+VDLATMREA+ +LGG+P +VNPLAPA++V
Sbjct: 63  AGWDPDAQPNTEIQFTPARVIMQDFTGVPCVVDLATMREAVKELGGDPKRVNPLAPAEMV 122

Query: 125 IDHSVIADLFGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTGIVHQVNIE 184
           IDHSV  D FG + A ERN+EIEYQRNGERYQFLRWGQ AFDDFKVVPPGTGIVHQVNIE
Sbjct: 123 IDHSVQIDAFGNSGALERNMEIEYQRNGERYQFLRWGQTAFDDFKVVPPGTGIVHQVNIE 182

Query: 185 YLASVVMTR--DGV--AYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSMLI 240
           YLA  VMTR  DGV  AYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSMLI
Sbjct: 183 YLARTVMTREIDGVLRAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSMLI 242

Query: 241 PRVVGFRLTGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRATLGNM 300
           PRVVGF+LTG I  G TATDVVLT+TE LR+HGVVGKFVEFYGEGVA VPLANRAT+GNM
Sbjct: 243 PRVVGFKLTGSIPAGATATDVVLTITEQLRKHGVVGKFVEFYGEGVAAVPLANRATIGNM 302

Query: 301 SPEFGSTAAIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDPKHEPEFSEYLELN 360
           SPEFGSTAA+FPID+ T+ YLR TGR+ E VALVE+YAK QG+WHD   E +FSEYLEL+
Sbjct: 303 SPEFGSTAAMFPIDDVTLDYLRLTGRSDENVALVESYAKEQGLWHDASREIKFSEYLELD 362

Query: 361 LSDVVPSIAGPKRPQDRIALAQAKSTFREQIYHYVG--NGSPDSPHDPHSKLDEVVEETF 418
           LS VVPSI+GPKRPQDRI L  AK  FR+ I++YV   +GS          +DE ++E+F
Sbjct: 363 LSTVVPSISGPKRPQDRIELTDAKEQFRKDIHNYVAIEDGS----------VDESLDESF 412

Query: 419 PASDPGQLTFANDDVATDETVHSAAAHADGRVSNPVRVKSDELGEFVLDHGAVVIAAITS 478
           PASD    T A+        V SAA  A GR SNPV +K+++  EF LDHGAV IA+ITS
Sbjct: 413 PASDAPSFTHADSHTTETSRVVSAANGAHGRPSNPVHIKTEDGREFELDHGAVSIASITS 472

Query: 479 CTNTSNPEVMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLEKLGF 538
           CTNTSNP VML AALLARNAV+KGLTSKPWVKT++APGS+VV DYY++SGL PYLEKLGF
Sbjct: 473 CTNTSNPSVMLAAALLARNAVDKGLTSKPWVKTSVAPGSKVVTDYYNKSGLTPYLEKLGF 532

Query: 539 YLVGYGCTTCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYLASPPL 598
           Y+VGYGC TCIGNSGPL  EIS+A+  NDLSVTAVLSGNRNFEGRINPDVKMNYLASPPL
Sbjct: 533 YIVGYGCATCIGNSGPLDAEISEAIQANDLSVTAVLSGNRNFEGRINPDVKMNYLASPPL 592

Query: 599 VIAYALAGTMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTRNYADV 658
           VIAYALAG+MDFDF T  LG+D+ G +VFL+DIWP+  +V   I ++I+++MF R Y  V
Sbjct: 593 VIAYALAGSMDFDFDTDSLGKDEAGNDVFLKDIWPNPVEVQQVIDSSIDKDMFARGYEGV 652

Query: 659 FKGDDRWRNLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALLGDSVT 718
           F GD RW+ L TP+G+TF WDPNSTYVRKPPYF+G+ A+PEPV +ISGARVL  LGDSVT
Sbjct: 653 FDGDARWKALDTPAGDTFAWDPNSTYVRKPPYFDGIKAQPEPVQDISGARVLLKLGDSVT 712

Query: 719 TDHISPAGAIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRNQLLDD 778
           TDHISPAG+ K  TPA +YL  +GV+RKD+NS+GSRRGNHEVMIRGTFANIR++NQ+LD 
Sbjct: 713 TDHISPAGSFKSDTPAGQYLLANGVERKDFNSYGSRRGNHEVMIRGTFANIRIKNQILDG 772

Query: 779 VSGGYTRDFTQPGGPQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTLLLGVR 838
           V GG+TRDFTQ  GPQA++YDAAQNY A   PLVV  GKEYGSGSSRDWAAKGT LLGV+
Sbjct: 773 VEGGFTRDFTQADGPQAYVYDAAQNYQAAGTPLVVLAGKEYGSGSSRDWAAKGTALLGVK 832

Query: 839 AVIAESFERIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKTPKTVC 898
           AV+AES+ERIHRSNLIGMGV+PLQFP G+SA++LGL GTE F + G+  LN+G TPKT+ 
Sbjct: 833 AVVAESYERIHRSNLIGMGVLPLQFPAGESAATLGLTGTETFAVEGVTALNEGTTPKTLK 892

Query: 899 VQATKGDGATIEFDAVVRIDTPGEADYYRNGGILQYVLRNI 939
           V AT  DG+   FDAV+RIDTPGEADYYRNGGILQYVLR I
Sbjct: 893 VTATAEDGSAKSFDAVLRIDTPGEADYYRNGGILQYVLRQI 933


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: 2570
Number of extensions: 99
Number of successful extensions: 3
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 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)
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