GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Caldicellulosiruptor hydrothermalis 108

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_013402598.1 CALHY_RS03330 3-isopropylmalate dehydratase large subunit

Query= BRENDA::P19414
         (778 letters)



>NCBI__GCF_000166355.1:WP_013402598.1
          Length = 429

 Score =  179 bits (454), Expect = 3e-49
 Identities = 140/450 (31%), Positives = 216/450 (48%), Gaps = 44/450 (9%)

Query: 57  RPFTYAEKILYGHLDDPHGQDIQRGVSYLKLRPDRVACQDATAQMAILQFMSAGLPQV-- 114
           +P T ++KIL  H     G++       +    D V   D T  +AI +F   G+ +V  
Sbjct: 3   KPMTMSQKILAYHA----GKEYVEPGDLIFANVDLVLGNDVTTPVAIKEFEKIGIDRVFD 58

Query: 115 AKPVTVHCDHLIQAQVGGEKDLKRAIDLNKEVYDFLASATAKYNM-GFWKPGS-GIIHQI 172
              + +  DH         KD+K A    K V +F      KY +  +++ G  GI H +
Sbjct: 59  KDKIAIVPDHFTP-----NKDIKSAQQC-KMVREF----AKKYEITNYFEVGEMGIEHAL 108

Query: 173 VLEN-YAFPGALIIGTDSHTPNAGGLGQLAIGVGGADAVDVMA-GRPWELKAPKILGVKL 230
           + E     PG L+IG DSHT   G LG  + G+G  D    MA G+ W  K P+ +   L
Sbjct: 109 LPEKGLVVPGDLVIGADSHTCTYGALGAFSTGIGSTDMACAMATGKCW-FKVPEAIKFVL 167

Query: 231 TGKMNGWTSPKDIILKLAGITTVKGGTGKIVEYFGDGVDTFSATGMGTICNMGAEIGATT 290
            GK  GWTS KDIIL + G+  V G   K +EY G+G+ + S     TI NM  E GA  
Sbjct: 168 YGKKTGWTSGKDIILHIIGMIGVDGALYKSMEYTGEGLKSLSMDDRFTIANMAIEAGAKN 227

Query: 291 SVFPFNKSMIEYLEATGRGKIADFAKLYHKDLLSADKDAEYDEVVEIDLNTLEPYINGPF 350
            +F  ++  IEY++           K Y   +  AD+DAEY EV EID++ ++P +  P 
Sbjct: 228 GIFEVDEKTIEYVKHHS-------TKPY--KIFKADEDAEYSEVYEIDISKIKPTVAFPH 278

Query: 351 TPDLATPVSKMKEVAVANNWPLDVRVGLIGSCTNSSYEDMSRSASIVKDAAAHGLKSKTI 410
            P+    + ++ E        + +   +IGSCTN   ED+  +A I+K      +K    
Sbjct: 279 LPENTKTIDEITE-------KIYIDQVVIGSCTNGRIEDLRIAAKILK---GRKVKKGLR 328

Query: 411 FTVTPGSEQIRATIERDGQLETFKEFGGIVLANACGPCIGQWDRRDIKKGDKNTIVSSYN 470
             + P ++ I     ++G +E F + G +V    CGPC+G      +  G+K   +++ N
Sbjct: 329 CIIFPATQNIYKQALKEGLIEIFIDAGCVVSTPTCGPCLG-GHMGILADGEK--ALATTN 385

Query: 471 RNFTSRNDGNPQTHAFVASPELVTAFAIAG 500
           RNF  R  G+P +  +++SP +  A A+ G
Sbjct: 386 RNFVGRM-GHPNSEVYLSSPAIAAASAVLG 414


Lambda     K      H
   0.317    0.136    0.405 

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: 798
Number of extensions: 33
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: 778
Length of database: 429
Length adjustment: 36
Effective length of query: 742
Effective length of database: 393
Effective search space:   291606
Effective search space used:   291606
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: 53 (25.0 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