GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Flavobacterium glycines Gm-149

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_066326079.1 BLR17_RS14020 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_900100165.1:WP_066326079.1
          Length = 427

 Score =  382 bits (981), Expect = e-110
 Identities = 208/418 (49%), Positives = 273/418 (65%), Gaps = 7/418 (1%)

Query: 374 LSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLT 433
           L RP +  ++I   V  I   V+  G++A+ +YT +FDGV   N  + A   E     ++
Sbjct: 16  LERPTKTVNDIEATVKEIFAAVQKDGDAAVAKYTTQFDGVYFENSEVTAAEIEVAINTIS 75

Query: 434 EEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPS 493
           +E+  A+ L+  NV KFH AQ  T  + +ET  GV C +  RPI+KVGLYIPGGTA L S
Sbjct: 76  DELTAAISLAKANVEKFHQAQKTTR-VSIETAEGVQCWQEKRPIQKVGLYIPGGTAPLFS 134

Query: 494 TALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAY 553
           T LML VPA++A C EIV  SPP K+ G ++P ++Y A   G +KI+  GG QA+A M +
Sbjct: 135 TVLMLAVPAKIAGCSEIVLCSPPDKN-GNINPAILYAANLCGVTKIIKVGGIQAIAGMTF 193

Query: 554 GTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVAS 613
           GT+ IPKV KI GPGNQ+VT AK   Q  TQ   +IDMPAGPSE+LV+AD+ A   FVAS
Sbjct: 194 GTKAIPKVYKIFGPGNQYVTVAK---QLATQFGVAIDMPAGPSELLVVADDTAVPAFVAS 250

Query: 614 DLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIVLCDG 673
           DLLSQAEHG+DSQVILV    S+  I  ++  +  Q   LPR  I  K IA+S  +  + 
Sbjct: 251 DLLSQAEHGVDSQVILVST--SKAMIDAVESEIQAQLELLPRKTIAEKAIANSKSIFVEN 308

Query: 674 YEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTY 733
              AL++ N+Y PEH I+  AN + YV  + NAGSVF+G YTPES GDY+SGTNHTLPT 
Sbjct: 309 DSIALDLINEYGPEHFIVCTANNDFYVDGIQNAGSVFIGNYTPESAGDYASGTNHTLPTN 368

Query: 734 GYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSKL 791
           GYA+ YSG N  +F K +T Q I+ +G++NIG A+  +A+ EGL  HRNAV +R+  L
Sbjct: 369 GYAKNYSGVNLDSFMKSMTFQKISEKGIQNIGTAIEVMAEAEGLQAHRNAVTLRLKSL 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: 757
Number of extensions: 30
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: 427
Length adjustment: 36
Effective length of query: 763
Effective length of database: 391
Effective search space:   298333
Effective search space used:   298333
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