GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3608455
          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:

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