GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Bacteroides thetaiotaomicron VPI-5482

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate 349729 BT0201 histidinol dehydrogenase (NCBI ptt file)

Query= SwissProt::P00815
         (799 letters)



>FitnessBrowser__Btheta:349729
          Length = 428

 Score =  371 bits (953), Expect = e-107
 Identities = 208/433 (48%), Positives = 283/433 (65%), Gaps = 7/433 (1%)

Query: 359 LDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNP 418
           + ++K   K    + L RP   T  +   V  II  VR +G+ A+LEY   FD V LS  
Sbjct: 2   MKLIKYPSKEQWAELLKRPALNTESLFDTVRTIINKVRAEGDKAVLEYEAAFDKVTLSAL 61

Query: 419 VLNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIE 478
            + +   ++    +++E+K A+ L+  N+  FH++Q      +VET  GV C +    IE
Sbjct: 62  TVTSEEIQKAEGLISDELKSAITLAKRNIETFHSSQRFVGK-KVETMEGVTCWQKAVGIE 120

Query: 479 KVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASK 538
           KVGLYIPGGTA L ST LML VPA++A C+EIV  +PP K+ G + P +++ A+  G SK
Sbjct: 121 KVGLYIPGGTAPLFSTVLMLAVPAKIAGCREIVLCTPPDKN-GNIHPAILFAAQLAGVSK 179

Query: 539 IVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEV 598
           I  AGG QA+AAMAYGTE++PKV KI GPGNQ+VTAAK  V     A   IDMPAGPSEV
Sbjct: 180 IFKAGGVQAIAAMAYGTESVPKVYKIFGPGNQYVTAAKQLVSLRDVA---IDMPAGPSEV 236

Query: 599 LVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDI 658
            V+AD  A+  FVA+DLLSQAEHG+DSQ +L+    SEK   E+ + V+ Q  +LPR +I
Sbjct: 237 EVLADASANPVFVAADLLSQAEHGVDSQAMLI--TTSEKLQAEVMEEVNRQLAKLPRREI 294

Query: 659 VRKCIAHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPES 718
             K + +S ++L    +EALE++N YAPEHLI++  N  +  + V NAGSVF+G+ TPES
Sbjct: 295 AAKSLENSKLILVKDMDEALELTNAYAPEHLIVETENYLEVAERVINAGSVFLGSLTPES 354

Query: 719 CGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLD 778
            GDY+SGTNHTLPT GYA+ YSG +  +F + IT Q I P+G++ IG A+  +A  E LD
Sbjct: 355 AGDYASGTNHTLPTNGYAKAYSGVSLDSFIRKITFQEILPQGMKVIGPAIEEMAANELLD 414

Query: 779 GHRNAVKIRMSKL 791
            H+NAV +R++ L
Sbjct: 415 AHKNAVTVRLNTL 427


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: 706
Number of extensions: 27
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 799
Length of database: 428
Length adjustment: 36
Effective length of query: 763
Effective length of database: 392
Effective search space:   299096
Effective search space used:   299096
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.

Links

Downloads

Related tools

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