GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Marinobacter adhaerens HP15

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate GFF2484 HP15_2428 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>FitnessBrowser__Marino:GFF2484
          Length = 434

 Score =  252 bits (643), Expect = 3e-71
 Identities = 147/424 (34%), Positives = 239/424 (56%), Gaps = 17/424 (4%)

Query: 373 ALSRPIQKTSEIMHLVNP----IIENVRDKGNSALLEYTEKFDGVKLSNPV---LNAPFP 425
           AL++ +     + H VN     I+  V+ +G+ A+LE+TEKFD +K+ +     ++    
Sbjct: 18  ALAKLLAWDDSVDHQVNESVRHILHEVKTRGDQAVLEFTEKFDRLKVGSVAELEMDQSRL 77

Query: 426 EEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIP 485
           ++  + + ++ + AL+ + E +R +H  Q   ++ + E + G +  +   P+++ GLY+P
Sbjct: 78  QQALDAIPQDQRVALEKAAERIRDYHERQ-NQKSWQYEDEDGTVLGQKVTPLDRAGLYVP 136

Query: 486 GGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGA 545
           GG A  PS+ LM  +PA+VA   E+V   P    DG V+  V+  A   G  ++   GGA
Sbjct: 137 GGKAAYPSSVLMNAIPAKVAGVSEVVMVVPT--PDGVVNDMVLASAAIAGVDRVFTVGGA 194

Query: 546 QAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADED 605
           QAV A+A+GTETIP VDKI+GPGN FV  AK     +   +  IDM AGPSE+LVI+D  
Sbjct: 195 QAVGALAFGTETIPAVDKIVGPGNIFVATAK----REVFGVVGIDMIAGPSEILVISDGK 250

Query: 606 ADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA- 664
            D D++A DL SQAEH   +Q IL+  +   + +  ++ +++     + R DI+R  +  
Sbjct: 251 TDPDWIAMDLFSQAEHDEQAQSILISPDA--EFLDAVEASINKLLPTMERADIIRTSMTD 308

Query: 665 HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSS 724
            + ++     ++A E+SN+ APEHL L + +    +  + +AG++F+G YT E+ GDY +
Sbjct: 309 RAALIHVTDLKQAAEVSNRIAPEHLELSVEDPEAMLDDIRHAGAIFMGRYTAEALGDYCA 368

Query: 725 GTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAV 784
           G NH LPT G AR  S      FQK  +    +  G + +GR    +A+ EGL  H  + 
Sbjct: 369 GPNHVLPTSGTARFSSPLGVYDFQKRSSIIGFSAAGADRMGRVASVLARGEGLTAHARSA 428

Query: 785 KIRM 788
           + R+
Sbjct: 429 EYRI 432


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: 669
Number of extensions: 31
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: 434
Length adjustment: 37
Effective length of query: 762
Effective length of database: 397
Effective search space:   302514
Effective search space used:   302514
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