GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Phyllobacterium endophyticum PEPV15

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_106717792.1 CU100_RS17230 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_003010935.1:WP_106717792.1
          Length = 434

 Score =  215 bits (547), Expect = 5e-60
 Identities = 144/418 (34%), Positives = 216/418 (51%), Gaps = 11/418 (2%)

Query: 378 IQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMK 437
           I + + +   V  ++  V   G+ A+   + +FDG+   +  L     +   + LT + +
Sbjct: 14  ISQDALLTKAVESLLTQVEKGGDEAVHALSVRFDGLDRRSYRLTDAEIKNCVDNLTRQQR 73

Query: 438 EALDLSIENVRKFHAAQLPT-ETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTAL 496
             +D + + VR F  AQ      +EVET PGV+      PI  VG Y+PGG   L ++A 
Sbjct: 74  ADIDFAQDQVRNFAQAQKNALRDIEVETLPGVVLGHKNVPIANVGCYVPGGKYPLLASAH 133

Query: 497 MLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTE 556
           M  + A+VA C+ ++  +PP   +G+++P +V      GA +I   GG QA+AAMA GTE
Sbjct: 134 MSVLTAKVAGCERVITCAPP--FNGEIAPLIVAAQHLAGADEIYCLGGVQAIAAMALGTE 191

Query: 557 TIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLL 616
           TI  VD + GPGN +V  AK  +         ID+ AGP+E LVIADE  D +  A+DLL
Sbjct: 192 TIDAVDMLAGPGNAYVAEAKRLLFGRV----GIDLFAGPTETLVIADETVDGEICATDLL 247

Query: 617 SQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH-STIVLCDGYE 675
            QAEHG++S  +L  +  SEK  ++    +      LP  +I RK       I++CD  E
Sbjct: 248 GQAEHGVNSPAVL--ITNSEKLARDTLREIDRLLEILPTREIARKAWEDCGEIIVCDTLE 305

Query: 676 EALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGY 735
           E +E++++ A EH+ +   +   ++  + N G++F+G  T  + GD   GTNHTLPT   
Sbjct: 306 EMVEVADRIASEHVQVMTRDPQYFLDRMKNYGALFLGQRTTVAYGDKVIGTNHTLPTKRA 365

Query: 736 ARQYSGANTATFQKFITAQNI-TPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSKLG 792
           AR   G     F K  T Q I T E    IG     ++  EG  GH     IR+ + G
Sbjct: 366 ARYTGGLWVGKFIKTCTYQKIVTDEASVLIGEYCSRLSIMEGFAGHAEQANIRVRRYG 423


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: 710
Number of extensions: 35
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 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