Alignments for a candidate for acn in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_1419 N515DRAFT_1419 aconitate hydratase

Query= SwissProt::O53166
         (943 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1419
          Length = 916

 Score = 1110 bits (2871), Expect = 0.0
 Identities = 569/946 (60%), Positives = 704/946 (74%), Gaps = 49/946 (5%)

Query: 6   VNSFGAHDTLKVGEKSYQIYRLDAVP---NTAKLPYSLKVLAENLLRNEDGSNITKDHIE 62
           ++SF   DTLKV   SYQI  L  +    +   LPYS+K+L ENLLR+EDG N+T   IE
Sbjct: 2   LDSFATRDTLKVNGSSYQIASLAKLGQRFDIKHLPYSMKILLENLLRHEDGVNVTAKEIE 61

Query: 63  AIANWDPKAEPSIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAPAD 122
           A+A W+PKAEP  EI + PARVV+QDFTGVPC+VDLA MR+A+  LGG+  ++NPLAPA+
Sbjct: 62  AVARWNPKAEPDTEIAFMPARVVLQDFTGVPCVVDLAAMRDAVVKLGGDAKQINPLAPAE 121

Query: 123 LVIDHSVIADLFGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTGIVHQVN 182
           LVIDHSV  D++G   A E+NV IE+QRN ERY FLRWGQ AFD+FKVVPP TGIVHQVN
Sbjct: 122 LVIDHSVQVDVYGSESALEQNVAIEFQRNQERYAFLRWGQKAFDNFKVVPPRTGIVHQVN 181

Query: 183 IEYLASVVMT--RDGV--AYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM 238
           +EYL  VV T  +DG   AYPDT  GTDSHTTM+NG+GVLGWGVGGIEAEAAMLGQP SM
Sbjct: 182 LEYLGRVVFTGEKDGQSWAYPDTVFGTDSHTTMINGVGVLGWGVGGIEAEAAMLGQPSSM 241

Query: 239 LIPRVVGFRLTGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRATLG 298
           LIP+VVGF+LTG++  GVTATD+VLTVT+MLR+ GVVGKFVEF+G G+ ++ LA+RAT+G
Sbjct: 242 LIPQVVGFKLTGKLAEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLKDLALADRATIG 301

Query: 299 NMSPEFGSTAAIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDPKH-EPEFSEYL 357
           NM+PE+G+T  IFP+D+E + YLR +GR+ E + LV+AYA+AQG+WHD      +F+  L
Sbjct: 302 NMAPEYGATCGIFPVDQEALNYLRLSGRSEEHIELVKAYAQAQGLWHDENTPHAQFTTTL 361

Query: 358 ELNLSDVVPSIAGPKRPQDRIALAQAKSTFREQIYHYVGNGSPDSPHDPHSKLDEVVEET 417
           EL+L DV PS+AGPKRPQDR+ L   + +FR+ +     N  P                 
Sbjct: 362 ELDLGDVRPSLAGPKRPQDRVLLQDVEKSFRDALGPLTANRRP----------------- 404

Query: 418 FPASDPGQLTFANDDVATDETVHSAAAHADGRVSNPVR---VKSDELGE-FVLDHGAVVI 473
                       N D  T   ++   + A G  +N V    V  ++ GE F L  GAVVI
Sbjct: 405 -----------RNGD--TSNFINEGGSAAIGNPANAVSESGVLVEKNGESFRLGDGAVVI 451

Query: 474 AAITSCTNTSNPEVMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYL 533
           AAITSCTNTSNP VMLGA LLA+ A  KGL ++PWVKT++ PGS+VV DY +++GL   L
Sbjct: 452 AAITSCTNTSNPAVMLGAGLLAKKAAAKGLKAQPWVKTSLGPGSKVVTDYLEKTGLLQEL 511

Query: 534 EKLGFYLVGYGCTTCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYL 593
           EK+GFY+VGYGCTTCIGNSGPLP EISK + + DL+V +VLSGNRNFEGR++P+VKMNYL
Sbjct: 512 EKVGFYVVGYGCTTCIGNSGPLPAEISKGIAEGDLAVASVLSGNRNFEGRVHPEVKMNYL 571

Query: 594 ASPPLVIAYALAGTMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTR 653
           ASPPLV+AYALAG++D D    PLG   DG+ V+LRDIWPS Q++SDTIA AIN  MF +
Sbjct: 572 ASPPLVVAYALAGSLDVDLSKDPLGTGSDGQPVYLRDIWPSNQEISDTIAGAINPAMFAK 631

Query: 654 NYADVFKGDDRWRNLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALL 713
           NYADVF+GDDRW ++ +P G+ ++W  +STY++ PPYF+GMT +   V +I GARVL L 
Sbjct: 632 NYADVFQGDDRWNHIASPDGSVYQWG-DSTYIKNPPYFDGMTREVGKVEDIHGARVLGLF 690

Query: 714 GDSVTTDHISPAGAIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRN 773
           GDS+TTDHISPAG+IK  +PA R+L   GV+ KD+NS+GSRRGN +VM+RGTFANIR+RN
Sbjct: 691 GDSITTDHISPAGSIKKDSPAGRFLIGKGVEPKDFNSYGSRRGNDDVMVRGTFANIRIRN 750

Query: 774 QLLDDVSGGYTRDFTQPGGPQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTL 833
            +LD V GGYT     P G Q  IYDAA  Y A+H PLVV  GKEYG+GSSRDWAAKGTL
Sbjct: 751 LMLDGVEGGYT--LHVPSGEQLAIYDAAMKYKAEHTPLVVLAGKEYGTGSSRDWAAKGTL 808

Query: 834 LLGVRAVIAESFERIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKT 893
           LLGV+AVIAESFERIHRSNL+GMGV+P QF +G+SA +LGL G EVFDITG   LNDG++
Sbjct: 809 LLGVKAVIAESFERIHRSNLVGMGVLPCQFEDGQSAQTLGLTGKEVFDITG---LNDGES 865

Query: 894 PKTVCVQATKGDGATIEFDAVVRIDTPGEADYYRNGGILQYVLRNI 939
            K   V AT  DG+  EF   V + TP E +++R+GGILQYVLR +
Sbjct: 866 -KVAKVTATAPDGSRKEFIVKVLLLTPKEREFFRHGGILQYVLRQL 910


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: 2418
Number of extensions: 137
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 943
Length of database: 916
Length adjustment: 43
Effective length of query: 900
Effective length of database: 873
Effective search space:   785700
Effective search space used:   785700
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 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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, or view the source code.

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