GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Marinicella litoralis KMM 3900

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_099019639.1 CCS90_RS11175 aconitate hydratase AcnA

Query= SwissProt::P37032
         (891 letters)



>NCBI__GCF_002591915.1:WP_099019639.1
          Length = 887

 Score = 1057 bits (2733), Expect = 0.0
 Identities = 518/889 (58%), Positives = 672/889 (75%), Gaps = 7/889 (0%)

Query: 6   DSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTKDI 65
           D+L T  QL  + K+Y Y+SL +    H   I+RLP+SLK+LLENLLR E+G  VT  DI
Sbjct: 3   DTLKTAMQLACNNKSYKYFSLAKIAETH--DISRLPFSLKILLENLLRNENGIDVTVSDI 60

Query: 66  KAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLSPV 125
           +A+ +W  N     EIAF P+RV++QDFTGVPAVVDLAAMR A+  +GG+  KI+PLSP 
Sbjct: 61  EALCNWDPNAAPATEIAFTPSRVVLQDFTGVPAVVDLAAMRDAMKALGGDVQKINPLSPA 120

Query: 126 DLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICHQV 185
           +LVIDHS+ VDK+ + D+ E+NT+IE +RN ERY FL+WGQ AF  F+VVPPG GI HQV
Sbjct: 121 ELVIDHSIQVDKYGTMDSAEINTQIEFQRNMERYGFLKWGQTAFDTFKVVPPGNGIVHQV 180

Query: 186 NLEYLGKTVWNSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVS 245
           NLEYL + ++ +E +G+L AYPDT+VGTDSHTTMING+GVLGWGVGGIEAEAAMLGQ +S
Sbjct: 181 NLEYLARVIFGAEKNGELMAYPDTVVGTDSHTTMINGIGVLGWGVGGIEAEAAMLGQAIS 240

Query: 246 MLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADRATI 305
           MLIP+V+GFKL+GK++EG+TATDLVLTV  MLR+ GVVGKFVEF+G GL  LPLADRATI
Sbjct: 241 MLIPQVVGFKLTGKMQEGVTATDLVLTVVDMLREHGVVGKFVEFFGSGLQHLPLADRATI 300

Query: 306 SNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVFTDS 365
           +NMAPEYGATCG FP+D E+++YL L+GR +  + LVEAYAKAQGM++D+++ +  +T  
Sbjct: 301 ANMAPEYGATCGIFPIDNESLRYLTLSGRSEEQVNLVEAYAKAQGMFHDENSIDAEYTAV 360

Query: 366 LHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNK--DFQMK 423
           L LD+ +V PS++GPKRPQD++ L+     +N    E  +     K+ AV +   ++   
Sbjct: 361 LELDMSTVVPSISGPKRPQDRIELTVAKETYNRHFKEF-ENGRAVKSVAVSSDRGNYDFT 419

Query: 424 HGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRHA 483
            G++ +AAITSCTNTSNP+V++ AGL+A+ A  KGL+ KPWVK+SLAPGSKVV+ YL  A
Sbjct: 420 DGNIAVAAITSCTNTSNPAVMLGAGLLARNAAAKGLKVKPWVKTSLAPGSKVVSHYLNAA 479

Query: 484 GLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHPQ 543
           G+   L+ LGFN+VG+GCTTCIGNSGPL   +S  + ++DL+ +SVLSGNRNFEGR+H  
Sbjct: 480 GVMDDLETLGFNVVGFGCTTCIGNSGPLDPALSKAINDNDLIATSVLSGNRNFEGRIHAD 539

Query: 544 VRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEVA-KVS 602
           ++ N+LASPPLVVAYA+ GT   DL  + +G+D+EGN VYL+DIWPSN EIA  +   VS
Sbjct: 540 IQMNFLASPPLVVAYAIAGTMDFDLQNDSLGEDQEGNPVYLRDIWPSNHEIADTIQNNVS 599

Query: 603 GTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIKQA 662
            T F + Y  +F+GDA+WQA++T+  + ++W  DSTYI++PP+F+ ++L+   +  I  A
Sbjct: 600 KTSFSEGYEGIFEGDANWQAVKTTESELFDWQGDSTYIKNPPYFDGMTLEVGTIDNISGA 659

Query: 663 YVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTFA 722
            VLA  GDS+TTDHISPAG+I   SPAG YLK KGV + +FNSYGSRRGNHEVMMRGTFA
Sbjct: 660 RVLAKLGDSVTTDHISPAGAIAEDSPAGSYLKEKGVPKVNFNSYGSRRGNHEVMMRGTFA 719

Query: 723 NIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWAA 782
           NIR+RN++ PG EGG TR+ P+ E MSI+DA+M+YQ     L++I G EYGTGSSRDWAA
Sbjct: 720 NIRLRNQLAPGTEGGWTRHQPSNEEMSIFDASMKYQAEGTPLLVIGGTEYGTGSSRDWAA 779

Query: 783 KGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIEISDKLT 842
           KGTNLLGVKAV+ +S+ERIHRSNL+GMG++PLQFK G +  T  L G E   +    K  
Sbjct: 780 KGTNLLGVKAVLVQSYERIHRSNLVGMGVIPLQFKAGESADTYDLTGKEVYDVS-GLKNG 838

Query: 843 PGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKISS 891
                 +T+ R+DG     E   RIDT  E+EY ++GGIL YVLR ++S
Sbjct: 839 ESKTAQITVHREDGSTVSFEVDVRIDTPKEVEYCRHGGILHYVLRNLAS 887


Lambda     K      H
   0.316    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: 2028
Number of extensions: 95
Number of successful extensions: 5
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: 891
Length of database: 887
Length adjustment: 43
Effective length of query: 848
Effective length of database: 844
Effective search space:   715712
Effective search space used:   715712
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