GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Rhodobacter ovatus JA234

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_097031410.1 CRO07_RS14595 aconitate hydratase AcnA

Query= SwissProt::P70920
         (906 letters)



>NCBI__GCF_900207575.1:WP_097031410.1
          Length = 894

 Score = 1129 bits (2921), Expect = 0.0
 Identities = 575/902 (63%), Positives = 685/902 (75%), Gaps = 18/902 (1%)

Query: 5   DSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVKKADI 64
           DS   +KTL VG  +Y YYS+P AE  GL   S+LP ++KV+LEN+LR EDG++V   DI
Sbjct: 8   DSQNTRKTLNVGGASYAYYSIPAAEAAGLGQFSRLPAALKVVLENMLRFEDGKTVSVDDI 67

Query: 65  VAVSKWLRKKSLE-HEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPLVP 123
            A S+W         EIA+RPARVLMQDFTGVPAVVDLAAMR+ +  LGGDA+KINPL P
Sbjct: 68  RAFSEWGANGGKNPREIAYRPARVLMQDFTGVPAVVDLAAMRDGILGLGGDAQKINPLNP 127

Query: 124 VDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGICHQ 183
           VDLVIDHSV+++ FG+ +AF  NV  EY++N ERY FLKWGQ AF+NF VVPPGTGICHQ
Sbjct: 128 VDLVIDHSVMIDEFGNPRAFQMNVDREYERNMERYTFLKWGQKAFNNFRVVPPGTGICHQ 187

Query: 184 VNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIEAE 243
           VNLEYL+QTVWT +++          EVAYPD+LVGTDSHTTMVNGLAVLGWGVGGIEAE
Sbjct: 188 VNLEYLAQTVWTDRDQ-------DGLEVAYPDTLVGTDSHTTMVNGLAVLGWGVGGIEAE 240

Query: 244 ACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLDH 303
           A MLGQP+SML+P VVGFKL G M EG TATDLVL V QMLRK GVVGKFVEF+G GLDH
Sbjct: 241 AAMLGQPVSMLIPEVVGFKLTGQMVEGTTATDLVLKVVQMLRKKGVVGKFVEFYGEGLDH 300

Query: 304 LSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRTAK 363
           L +AD+ATIANMAPEYGATCGFFP+DA  + YL+ +GR   R+ALV+AYAKA G++R   
Sbjct: 301 LPLADRATIANMAPEYGATCGFFPIDAETLRYLRQTGRDEARIALVEAYAKANGMWRDEG 360

Query: 364 SADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAKRFAV 423
            A P++T+TL LD++++VP+++GPKRP+  + L      F+  +   +K+ +   K   V
Sbjct: 361 YA-PIYTDTLHLDMSEIVPAISGPKRPQDYLPLTEAKASFAKEMEATFKRPQ--GKEVPV 417

Query: 424 EGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAPGSQV 483
           +G+ Y +  G VVIA+ITSCTNTSNP VLIGAGL+AR A A GL  KPWVKTSLAPGSQV
Sbjct: 418 KGEDYTMSSGKVVIASITSCTNTSNPYVLIGAGLVARKARALGLNRKPWVKTSLAPGSQV 477

Query: 484 VAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLSGNRN 543
           V+ YL  +GLQ  LD +GFNLVG+GCTTCIGNSGPL  EIS +I +  +VA AVLSGNRN
Sbjct: 478 VSEYLEAAGLQEDLDAIGFNLVGYGCTTCIGNSGPLQPEISAAIAEGDLVATAVLSGNRN 537

Query: 544 FEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTSKEIN 603
           FEGR+SPDV+ANYLASPPLVVA+ALAG +  +L  EP+G G +G PVYLKDIWPT+ EI 
Sbjct: 538 FEGRISPDVRANYLASPPLVVAYALAGDMNIDLTSEPIGMGTNG-PVYLKDIWPTNAEIA 596

Query: 604 AFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMKKEPE 663
             + + VT   F KKYADVFKGD  W+ ++T +SETY W  SSTY+QNPPYF  M K+P 
Sbjct: 597 ELVDRCVTREAFLKKYADVFKGDAKWQAVETTDSETYDWPPSSTYIQNPPYFRNMSKKPG 656

Query: 664 PVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRGNHE 723
            +T+I  AR+LA+ GD ITTDHISPAGS K T+PAGKYL +  V P +FN YG RRGNHE
Sbjct: 657 VITNITGARVLALLGDMITTDHISPAGSFKDTTPAGKYLVDRGVAPREFNSYGARRGNHE 716

Query: 724 VMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLVVFAG 783
           VMMRGTFANIRIKN ML G +G    G      PDG Q SIYDA+M YQ    PLV+F G
Sbjct: 717 VMMRGTFANIRIKNEMLDGVEGGYTLG------PDGVQTSIYDASMAYQAAGTPLVIFGG 770

Query: 784 AEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSLGLKG 843
            EYG GSSRDWAAKGT LLGV+AVI +SFERIHRSNLVGMGV+P  F EG +  SLGLKG
Sbjct: 771 IEYGAGSSRDWAAKGTALLGVKAVIAESFERIHRSNLVGMGVIPFEFTEGQTRKSLGLKG 830

Query: 844 DEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILHYVLRK 903
           DE VT+ GL GDLKP   +   I  GDG+++ + L CRIDT  E++Y  +GG+LHYVLR 
Sbjct: 831 DEVVTIEGLDGDLKPLSLVPCTITYGDGTVKAIQLKCRIDTEIEIEYVEHGGVLHYVLRD 890

Query: 904 LA 905
           LA
Sbjct: 891 LA 892


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: 2146
Number of extensions: 93
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: 906
Length of database: 894
Length adjustment: 43
Effective length of query: 863
Effective length of database: 851
Effective search space:   734413
Effective search space used:   734413
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: 56 (26.2 bits)

This GapMind analysis is from Sep 24 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