GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Dinoroseobacter shibae DFL-12

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 3608455 Dshi_1851 aconitate hydratase 1 (RefSeq)

Query= SwissProt::P70920
         (906 letters)



>lcl|FitnessBrowser__Dino:3608455 Dshi_1851 aconitate hydratase 1
           (RefSeq)
          Length = 928

 Score = 1109 bits (2868), Expect = 0.0
 Identities = 568/928 (61%), Positives = 694/928 (74%), Gaps = 41/928 (4%)

Query: 5   DSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDG-RSVKKAD 63
           D+ K +KTL+VG ++  YYS+P AE  GL   SKLP ++KV+LEN+LR EDG R+V   D
Sbjct: 8   DTAKTRKTLRVGDQSLAYYSIPAAETAGLGDFSKLPAALKVVLENMLRFEDGGRTVSVDD 67

Query: 64  IVAVSKWLRKKSLE-HEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPLV 122
           I A + W  K      EIA+RPARVLMQDFTGVPAVVDLAAMR+ +  LGGDAEKINPL 
Sbjct: 68  IRAFADWADKGGQNPREIAYRPARVLMQDFTGVPAVVDLAAMRDGIVGLGGDAEKINPLN 127

Query: 123 PVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGICH 182
           PVDLVIDHSV+++ FG+ +AF  NV  EY++N ERY FLKWGQ+AF+NF VVPPGTGICH
Sbjct: 128 PVDLVIDHSVMIDEFGNPRAFQMNVDREYERNIERYTFLKWGQSAFANFRVVPPGTGICH 187

Query: 183 QVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIEA 242
           QVNLEYL+Q VWT  ++          EVAYPD+LVGTDSHTTMVNG+AVLGWGVGGIEA
Sbjct: 188 QVNLEYLAQAVWTDTDQSGQ-------EVAYPDTLVGTDSHTTMVNGMAVLGWGVGGIEA 240

Query: 243 EACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLD 302
           EA MLGQP+SML+P VVGF+L G M EG T TDLVL V +MLR  GVVGKFVEF+G GLD
Sbjct: 241 EAAMLGQPISMLIPEVVGFELTGEMMEGTTGTDLVLKVVEMLRAKGVVGKFVEFYGAGLD 300

Query: 303 HLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRTA 362
           HL +AD+ATIANMAPEYGATCGFFP+D   + Y++T+GR   R+ALV+AYAK  GL+R  
Sbjct: 301 HLPLADRATIANMAPEYGATCGFFPIDGETLRYMRTTGRDEARIALVEAYAKENGLWRGD 360

Query: 363 KSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVAL--------ANEYKKT 414
             A PV+T+TL+LD+  +VP+++GPKRP+  +AL   AE F   +        A+E  K 
Sbjct: 361 DYA-PVYTDTLSLDMGTIVPAISGPKRPQDYVALDKAAETFRDYVTGQRPDWSADEEDKA 419

Query: 415 E-----------------EPAKRFAVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGL 457
           E                    KR  V G  Y I  G +VIA+ITSCTNTSNP V+IGAGL
Sbjct: 420 EWTDEGGAVAPRDIPGDRGKHKRARVRGADYTIHDGTIVIASITSCTNTSNPYVMIGAGL 479

Query: 458 LARNAAAKGLKAKPWVKTSLAPGSQVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSG 517
           +AR A A GL  KPWVKTSLAPGSQVV+AYL  +GLQ  LD +GFNLVG+GCTTCIGNSG
Sbjct: 480 VARKARALGLTRKPWVKTSLAPGSQVVSAYLEAAGLQEDLDAIGFNLVGYGCTTCIGNSG 539

Query: 518 PLPEEISKSINDNGIVAAAVLSGNRNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLA 577
           P+ EE+S++IND  I+A +VLSGNRNFEGR+SPDV+ANYLASPPLVVA+ALAG +  +L 
Sbjct: 540 PIQEELSEAINDGDIIATSVLSGNRNFEGRISPDVRANYLASPPLVVAYALAGDMNVDLT 599

Query: 578 VEPLGEGKDGKPVYLKDIWPTSKEINAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVES 637
            +PLG+ +DG  VYLKDIWP++KEI   +++ VT   F+ KYADVFKGD  W+ ++T +S
Sbjct: 600 RDPLGQDRDGNDVYLKDIWPSTKEIAELVEQTVTREAFQAKYADVFKGDEKWQSVETTDS 659

Query: 638 ETYRWNMSSTYVQNPPYFEGMKKEPEPVTDIVEARILAMFGDKITTDHISPAGSIKLTSP 697
            TY W  SSTYVQNPPYF+GM  EP  +++I  A+ILA+ GD ITTDHISPAGS K ++P
Sbjct: 660 LTYDWPPSSTYVQNPPYFQGMSAEPGTISNIEGAKILAILGDMITTDHISPAGSFKESTP 719

Query: 698 AGKYLSEHQVRPADFNQYGTRRGNHEVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWP 757
           AG+YL+E QV+P +FN YG+RRGNHEVMMRGTFANIRI+N ML G +G    G      P
Sbjct: 720 AGRYLTERQVQPREFNSYGSRRGNHEVMMRGTFANIRIRNEMLDGVEGGYTLG------P 773

Query: 758 DGEQMSIYDAAMKYQQEQVPLVVFAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHR 817
           DG+Q SI++AAM YQ+   PLV+F G +YG GSSRDWAAKGT LLGV+AVI +SFERIHR
Sbjct: 774 DGQQTSIFEAAMAYQEMGTPLVIFGGEQYGAGSSRDWAAKGTSLLGVKAVIAESFERIHR 833

Query: 818 SNLVGMGVLPLTFEEGTSWSSLGLKGDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVS 877
           SNLVGMGV+P  F  G +  +LGLKGDE V++ GL G + P  ++   I  GDG+ + ++
Sbjct: 834 SNLVGMGVIPFEFTGGDTRKTLGLKGDETVSITGLDGKIVPLSEMPCTITYGDGTTREIT 893

Query: 878 LLCRIDTLDELDYYRNGGILHYVLRKLA 905
           L CRIDT  E++Y  NGG+LHYVLR LA
Sbjct: 894 LKCRIDTEVEIEYIENGGVLHYVLRNLA 921


Lambda     K      H
   0.317    0.134    0.393 

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: 2226
Number of extensions: 111
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 906
Length of database: 928
Length adjustment: 43
Effective length of query: 863
Effective length of database: 885
Effective search space:   763755
Effective search space used:   763755
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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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:

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:

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:

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