GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Thermophagus xiamenensis HS1

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_010527284.1 GQW_RS0106975 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_000220155.1:WP_010527284.1
          Length = 426

 Score =  386 bits (991), Expect = e-111
 Identities = 210/417 (50%), Positives = 280/417 (67%), Gaps = 9/417 (2%)

Query: 376 RPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEE 435
           R I    E+M  V PI++ V+   + AL E T +FDG++LSN  +     ++    +  +
Sbjct: 18  RAIVDQQEVMEKVKPILQAVKQHKDKALQELTAQFDGIELSNFEVTEEEIKQGCLDVDSQ 77

Query: 436 MKEALDLSIENVRKFHAAQ-LPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPST 494
           +K A++ +  N+R FH +Q LP +  ++ET PGV C +   PIEKVGLYIPGG+A L ST
Sbjct: 78  LKGAINSARINIRHFHESQQLPIK--KIETTPGVQCWQRSTPIEKVGLYIPGGSAPLFST 135

Query: 495 ALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYG 554
            LML +PA +A CKEIV  SPP K +GK+ P +++ A   G +KI   GGAQA+AAMAYG
Sbjct: 136 VLMLAIPATIAGCKEIVLCSPPDK-EGKIHPAILFAAHLTGVTKIFKVGGAQAIAAMAYG 194

Query: 555 TETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASD 614
           TETIPKVDKI GPGN FVTAAK  V  D  A   ID+PAGPSEV V+ADE A  +FVASD
Sbjct: 195 TETIPKVDKIFGPGNSFVTAAKQLVTLDGIA---IDLPAGPSEVAVMADESAHPEFVASD 251

Query: 615 LLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIVLCDGY 674
           LLSQAEHG DSQ IL+    SE+   ++  A++ Q   LPR+   +K + +S I+L    
Sbjct: 252 LLSQAEHGPDSQSILI--TDSEQLANDVTIAINEQLKSLPRIYTAKKALENSRIILLSNL 309

Query: 675 EEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYG 734
           +E ++ SN YAPEHLIL + N N   + + NAGSVF+G +TPES GDY+SGTNHTLPTYG
Sbjct: 310 DEMIDFSNLYAPEHLILAVRNPNYVAEKITNAGSVFLGHFTPESAGDYASGTNHTLPTYG 369

Query: 735 YARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSKL 791
           YAR YSG N  +F K IT Q IT +GL+ +G  +  +A+ E L+ H+ A+ +R++K+
Sbjct: 370 YARAYSGVNLDSFCKKITFQEITKDGLKKLGPIIETMAEAEQLEAHKMAISVRLNKI 426


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: 738
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: 799
Length of database: 426
Length adjustment: 36
Effective length of query: 763
Effective length of database: 390
Effective search space:   297570
Effective search space used:   297570
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