GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Oleispira antarctica RB-8

Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_046009357.1 OLEAN_RS11565 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>NCBI__GCF_000967895.1:WP_046009357.1
          Length = 928

 Score =  328 bits (842), Expect = 7e-94
 Identities = 283/926 (30%), Positives = 431/926 (46%), Gaps = 113/926 (12%)

Query: 4   EYRKHVAERAAQ-GIVPKPLD-ATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEAA 61
           EY + +  R    G+ PKP+D A  ++ ++  +K       E  LD  I    PG   AA
Sbjct: 6   EYLEEIEVRKNDLGLNPKPIDTADLLSEIIAQIKDTGNAAREASLDFFIYNTIPGTTSAA 65

Query: 62  YVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLID-ALDDAKLAPIAAKALS 120
            VKA FL  +A G  T   ++PE A+E L  M+GG ++  L+D AL D   A  A + L 
Sbjct: 66  VVKAAFLKDIALGTETVAEITPEFALEQLSHMKGGPSVEALLDIALSDDAQAKAAGEVLK 125

Query: 121 HTLLMFD-NFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKI-TVTVFKVTGETN 178
             + +++ +   + +  KAGN  AK +++S+A AE+F   P +  KI  VT     G+ +
Sbjct: 126 SQVFLYEADTSRIADAFKAGNAIAKDLLESYAAAEFFTKLPEIPAKIDVVTYIAAEGDIS 185

Query: 179 TDDLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGD 238
           TD LSP   + SR D  LH Q M+    +  E    G   P  ++  + +KG        
Sbjct: 186 TDLLSPGNQSHSRADRELHGQCMITPEAQQ-EIVALGKKHPNAKVMLIAEKG-------- 236

Query: 239 VVGTGSSRKSATNSV-LWFMGDDIPNVPNKRGGGLCLGGK-IAPIFF------------- 283
            +G GSSR S  N+V LW      P +P      +  G   IAPIF              
Sbjct: 237 TMGVGSSRMSGVNNVALWAGEKTSPYIPFINNAPVVAGTNGIAPIFLTTVGVTGGIGLDL 296

Query: 284 -----------NTMEDAGALPIEVDVSNLNMGDVIDVYPYKGEVRNHETGELLATFELKT 332
                      NT++DA    +  +  ++  G V+ +     ++ N +  EL+   +  +
Sbjct: 297 KNWVKKVDAEGNTVKDANGDNVLEEAYSVATGTVLTIDTAAKKLYNGDK-ELVDVSDAFS 355

Query: 333 DVLIDEVRAGGRIPLIIGRGLTTKAREALGLPHSDVFRQAKDVAESSRGFSLAQKMVGR- 391
              ++ ++AGG   L  G+ L T A E LG+    VF  +K+++   +G +  +K+  R 
Sbjct: 356 PQKVEFMKAGGSYALTFGKKLQTFAAETLGIQAPTVFAPSKEISVEGQGLTAVEKIFNRN 415

Query: 392 ACGVKGIRP---GAYCEPKMTSVGSQDTTGPMTRDELKDLAC--LGFSADLVMQSFCHTA 446
           A GV    P   G+    K+  VGSQDTTGPMT  EL+ +A   +  S D   QS CHTA
Sbjct: 416 AVGVASSTPLHTGSDVRVKVNIVGSQDTTGPMTCQELESMAASTISPSVDGAFQSGCHTA 475

Query: 447 AYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIHSW-------LNRMLLPD-TVGTGGDS 498
           +            L  F+ + G ++ R   GV HS        LN + + D  +  GGDS
Sbjct: 476 SVWDNKAKANTPKLMAFMNDFGVITARDPKGVYHSMTDVIHKVLNDITIDDRAIIIGGDS 535

Query: 499 HTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVHAIPLYAI 558
           HTR   G++F A SG VA A ATG   + +PESV V FKG+M+  I  RD+VH+     +
Sbjct: 536 HTRMSKGVAFGADSGTVAIALATGECAMPIPESVKVTFKGQMKDHIDFRDVVHSTQAQML 595

Query: 559 KQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTIKLNKEPIVE 618
                    K  +N+F GR++E++ +  L  +QAF  TD +AE  A         + +V+
Sbjct: 596 --------NKFGENVFQGRVIEVQ-IGTLLADQAFTFTDWTAEMKAKASICISTDDTLVQ 646

Query: 619 YLTSNIVLLKWMIAEGYGDRRTL--------ERRIQGMEKWLADPQLLEADADAEYAAVI 670
            L  +   ++ MI +G  +   +        ++RI G++    +   L  D  A Y A +
Sbjct: 647 SLELSKARIQIMINKGMDNATNMLQGLIDLADKRIAGIQS--GEEPALAPDDTATYFAEM 704

Query: 671 DIDLADIKEPILCAP---NDPDDARLLSDV-------QGEKIDEVFIGSCMTNIGHFRAA 720
            +DL  I EP++  P   N+    R   DV        G K+D  F+GSCM + G  +  
Sbjct: 705 VVDLDLIDEPMIADPDVNNEDASKRYTHDVIRQASFYDGRKVDLGFVGSCMVHKGDMQII 764

Query: 721 GKLLDNHKGQLP----TRLWVAPPTRMDAAQLTEEGYYSVFG------------KSGAR- 763
             +L N +   P    + L VAPPT     +L  EG + V              K  AR 
Sbjct: 765 AAMLRNLEKNGPITFNSPLVVAPPTYNIVDELKAEGDWEVLAKYAGFTFDDSHPKEAART 824

Query: 764 -------IEIPGCSLCMGNQARVADGATVVSTSTRNFPNRLGTGA-----NVFLASAELA 811
                  +E PGC+LCMGNQ +   G TV++TSTR F  R+   +        L S  + 
Sbjct: 825 KYENIMYLERPGCNLCMGNQEKAEAGDTVLATSTRLFQGRVVEDSTEKKGESLLGSTPMV 884

Query: 812 AVAALIGKLPTPEEYQTYVAQVDKTA 837
            +A+++G+ PT  EY+  V  ++ T+
Sbjct: 885 VLASILGRFPTIAEYKAAVEGINLTS 910


Lambda     K      H
   0.317    0.136    0.400 

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: 1710
Number of extensions: 84
Number of successful extensions: 11
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: 865
Length of database: 928
Length adjustment: 43
Effective length of query: 822
Effective length of database: 885
Effective search space:   727470
Effective search space used:   727470
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 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. 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