GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Shewanella loihica PV-4

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate 5209745 Shew_2198 histidinol dehydrogenase (RefSeq)

Query= SwissProt::P00815
         (799 letters)



>FitnessBrowser__PV4:5209745
          Length = 443

 Score =  355 bits (912), Expect = e-102
 Identities = 195/422 (46%), Positives = 272/422 (64%), Gaps = 9/422 (2%)

Query: 371 QKALSR-PIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYF 429
           ++ALSR P+   + +   V  II+ V  +G+ AL  +++KFD V+L    L+        
Sbjct: 25  REALSRSPLIGDANLEQQVKAIIDQVASQGDVALKAFSQKFDKVELDALRLSDAAIAAAS 84

Query: 430 EGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTA 489
           E +T E+K A++ + +N+  FH AQ   + +++ETQ GV C     PIEKVGLYIPGG+A
Sbjct: 85  ERVTPEIKAAIEQAKQNIETFHQAQA-FKGIDLETQAGVRCELRSEPIEKVGLYIPGGSA 143

Query: 490 ILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVA 549
            L ST LML +PA++A C++ V  SPP   D      +VY A+  G + I   GGAQA+A
Sbjct: 144 PLISTVLMLALPAKIAGCEQRVLVSPPPIDDA-----IVYAAKACGITDIYQIGGAQAIA 198

Query: 550 AMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVD 609
           A+A GTE++P VDKI GPGN++VT AK  V  D++ + SIDMPAGPSEVLVIAD +A+ D
Sbjct: 199 ALAQGTESVPAVDKIFGPGNRYVTEAKRLVAQDSRCVVSIDMPAGPSEVLVIADNEANPD 258

Query: 610 FVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIV 669
           F+A+DLLSQAEHG DSQV+LV    S+     +  ++  Q  +LPR +I  + ++ S  +
Sbjct: 259 FIAADLLSQAEHGPDSQVMLV--TDSQTLADAVNQSLGEQLARLPRAEIAMQALSASRTL 316

Query: 670 LCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHT 729
           + +   +A E+SN+Y PEHLI+Q       +  +  AGSVF+GAYTPES GDY+SGTNH 
Sbjct: 317 IVEDMAQAAEVSNRYGPEHLIIQTRAPRKLLSKIRAAGSVFLGAYTPESVGDYASGTNHV 376

Query: 730 LPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789
           LPTYGY+R  S  + A F +  T Q ++ EGL  +G  VM +A  E LD HRNAV +R++
Sbjct: 377 LPTYGYSRAVSSLSLADFSRRFTVQELSAEGLRGLGECVMTLASAEQLDAHRNAVAVRLA 436

Query: 790 KL 791
            L
Sbjct: 437 TL 438


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: 659
Number of extensions: 24
Number of successful extensions: 4
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: 443
Length adjustment: 37
Effective length of query: 762
Effective length of database: 406
Effective search space:   309372
Effective search space used:   309372
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 Aug 03 2021. The underlying query database was built on Aug 03 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