GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Desulforamulus ruminis DSM 2154

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_013841335.1 DESRU_RS06590 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_000215085.1:WP_013841335.1
          Length = 432

 Score =  301 bits (771), Expect = 5e-86
 Identities = 171/434 (39%), Positives = 261/434 (60%), Gaps = 13/434 (2%)

Query: 359 LDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNP 418
           + +++ SD  G++  L         I   V  I++ VR++G+ AL  +T +FDG  L+  
Sbjct: 2   IKIIEVSDSEGLKALLKGRSGGQEGIASRVAAIMQEVRERGDIALCGFTRRFDGASLTPE 61

Query: 419 VLNAPFPE--EYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRP 476
            L     E  + +  + +E+  +L L+ + +RK+H  QL     + E   G L  +   P
Sbjct: 62  QLRVTDEEIDQAYSMVDQEVLTSLKLARDRIRKYHQKQLTRSWFDTEPN-GTLLGQLITP 120

Query: 477 IEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGA 536
           +++VG+Y+PGGTA  PS+ LM  VPA+VA   ++V  +PP  +DGK++P  +  A + G 
Sbjct: 121 LDRVGVYVPGGTASYPSSVLMNAVPAKVAGVSQVVMVTPPG-ADGKLNPYTLVAAREAGV 179

Query: 537 SKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPS 596
            +I  AGGAQA+AA+AYGTETI  VDKI GPGN FVT AK  V         IDM AGPS
Sbjct: 180 DEIYKAGGAQAIAALAYGTETIAPVDKITGPGNIFVTLAKRMVYGQVD----IDMLAGPS 235

Query: 597 EVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQE-IQDAVHNQALQLPR 655
           EVLV+AD  A+ ++ A+D+LSQAEH + +  +L+      +++ E ++  +  Q   LPR
Sbjct: 236 EVLVVADASANPEYAAADMLSQAEHDVLASAVLL---THHRELAEWVRQELEKQVALLPR 292

Query: 656 VDIVRKCIA-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAY 714
            D+ R+ +A HS +V+    EE+LE++N +APEHL L +     ++  + +AG+VF+GA+
Sbjct: 293 QDLAREALANHSALVITGSLEESLELANAFAPEHLELLVEEPFRWLSRIRHAGAVFLGAH 352

Query: 715 TPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKK 774
           +PE  GDY +G NH LPT G AR YS  N  TF K  +  + + E LE +G  ++ +A+ 
Sbjct: 353 SPEPVGDYLAGPNHVLPTGGTARFYSPLNVDTFMKKSSIISFSKENLELLGPDIIRLAEV 412

Query: 775 EGLDGHRNAVKIRM 788
           EGL  H NAV++R+
Sbjct: 413 EGLQAHANAVRVRL 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: 697
Number of extensions: 38
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: 432
Length adjustment: 37
Effective length of query: 762
Effective length of database: 395
Effective search space:   300990
Effective search space used:   300990
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 25 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