GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisI in Caldicellulosiruptor kronotskyensis 2002

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_013430204.1 CALKRO_RS06255 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_000166775.1:WP_013430204.1
          Length = 431

 Score =  244 bits (622), Expect = 9e-69
 Identities = 157/424 (37%), Positives = 232/424 (54%), Gaps = 14/424 (3%)

Query: 370 VQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFD--GVKLSN-PVLNAPFPE 426
           ++ A  R  +   EI   V  II +V+DK + ALL YT  FD  G+ L+   V+      
Sbjct: 14  IETAKIRKWENEEEIEQKVRRIISDVKDKKDEALLYYTRMFDCKGICLNELRVVQEEIER 73

Query: 427 EYFEGLTEE--MKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYI 484
            YFE   E+    +AL+ + +N+ ++H  Q       ++   G L  +   P+EKVG+Y+
Sbjct: 74  AYFECEKEDGDFIDALNAAYKNIYEYHMRQKEESWFYIKN--GSLLGQIIMPLEKVGIYV 131

Query: 485 PGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGG 544
           PGG    PST LM  +PA+VA  ++I+  +PP K+   +S   +  A+  G  +I   GG
Sbjct: 132 PGGKGAYPSTVLMNSIPAKVAGVEKIIMVTPPDKNKS-ISKYTLAAAKICGIDEIYKVGG 190

Query: 545 AQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADE 604
           AQAVAA+A+GT+ IPKVDKI+GPGN +V  AK  +         ID  AGPSEV+VIADE
Sbjct: 191 AQAVAALAFGTQIIPKVDKIVGPGNIYVATAKKLLFG----YVDIDSVAGPSEVMVIADE 246

Query: 605 DADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA 664
            A+  ++A+DLLSQAEH   ++ ILV  +L  +  QE+ + V     +            
Sbjct: 247 SANPKYIAADLLSQAEHDPMARCILVTTSL--QVAQEVSENVDKMLARFENSVAFEAIEK 304

Query: 665 HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSS 724
           +  I++ D   EA E++N  APEHL +   +A   +  + NAG+VFVG Y+PE  GDY +
Sbjct: 305 NGVIIVVDDLFEAAEIANIIAPEHLEICCNDAEKVLFKIRNAGAVFVGEYSPEPIGDYIA 364

Query: 725 GTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAV 784
           G NH LPT G A  +S      F K ++    + E         + +A+KEG   H N++
Sbjct: 365 GPNHVLPTSGTASFFSPLGVYDFVKRMSLIKYSKEQFLTDAPHAINIAQKEGFLFHANSL 424

Query: 785 KIRM 788
           K+R+
Sbjct: 425 KVRL 428


Lambda     K      H
   0.315    0.133    0.371 

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: 806
Number of extensions: 55
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: 799
Length of database: 431
Length adjustment: 37
Effective length of query: 762
Effective length of database: 394
Effective search space:   300228
Effective search space used:   300228
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: 42 (22.0 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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