GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Streptacidiphilus oryzae TH49

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_037570494.1 BS73_RS07155 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000744815.1:WP_037570494.1
          Length = 577

 Score =  317 bits (811), Expect = 1e-90
 Identities = 208/516 (40%), Positives = 294/516 (56%), Gaps = 33/516 (6%)

Query: 41  GMDDEDFA-KPQIGVASSWNEITPCNLSLDRLANAVKEGVFSAGGYPLEFGTISVSDGIS 99
           G+ D+ F  +PQI +A++ +++TPCN  LD +A AV++GV  AGG  L    +S+ + + 
Sbjct: 33  GLPDDAFTGRPQIAIANTASDLTPCNSHLDEVAAAVRDGVHEAGGIALNLPVVSLGETLL 92

Query: 100 MGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDKSLPGMLMAAARLDLAAVFLY 159
                   +++ R + A S E +++   +DG+VLL GCDK++P +LMAAA +DL +V + 
Sbjct: 93  KPT-----AMLWRNMAAMSTEEMLRGNPVDGAVLLGGCDKTIPSLLMAAASVDLPSVVVP 147

Query: 160 AGSILPGRAK---LSDGSERDVTIIDAFEAVGACSRGLMSRADVDAIERAICPGEGACGG 216
            G +L G  +   L  G+       D +        G +S  D  A E A+    G C  
Sbjct: 148 GGPMLTGTFRGRPLGCGT-------DVWRLSEEVRSGELSAEDFTASESAMIRSRGHCNT 200

Query: 217 MYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVELLRRGITARDILTKEA 276
           M TA+TM   AEALG  LPG+A  PA D R    AR SG+  VE++R       +LT+ +
Sbjct: 201 MGTASTMGLLAEALGTVLPGTAGIPAPDSRLLRAARESGRLAVEMVRADRRPSTLLTEGS 260

Query: 277 FENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRIGSGVPHLADVKPFGRHVMSD 336
           F NAI  + A GGSTNAV+HLLAIA    + LSL DF RIGSGVP L D++P GR++M D
Sbjct: 261 FRNAIVALAALGGSTNAVVHLLAIAGRLGIPLSLDDFDRIGSGVPLLTDLQPAGRYLMED 320

Query: 337 VDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENL--AAITPPDPDGKVLRALANPIHP 394
           +   GG+  V++ + D  LL  + LTVTG  +A  L  A I     D +V+R    P+ P
Sbjct: 321 LHRAGGLHAVLREVRD--LLDPEALTVTGRPLAGYLDDARIW----DTEVIRERERPLQP 374

Query: 395 SGGITILHGSLAPEGAVVKTAGFDSDVF--EGTARVFDG---ERAALDALEDGTITVGDA 449
             GI +L G+LAP+GAV+K A    ++    G A VFD     RA +D   D  +     
Sbjct: 375 DAGIAVLRGNLAPDGAVIKPAAATPELLSHRGRAMVFDSIEDFRARVDD-PDLDVDADTV 433

Query: 450 VVIRYEGPKGGPGMREM--LAITGAIKGAGLGKDVLLLTDGRFSGGTTGLCVGHIAPEAV 507
           +V+R  GPKG PGM E+  L +   +   G+ +D++ + DGR SG   G  V H+APEA 
Sbjct: 434 LVLRGCGPKGYPGMPEVSNLPLPPKLLRQGV-RDMVRICDGRMSGTAYGTVVLHVAPEAA 492

Query: 508 DGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQ 543
            GGP+AL+R GD I LDVA R L+V     E A+R+
Sbjct: 493 AGGPLALIRTGDWIELDVAARTLNVDLPAEELAARK 528


Lambda     K      H
   0.318    0.136    0.393 

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: 947
Number of extensions: 49
Number of successful extensions: 6
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: 575
Length of database: 577
Length adjustment: 36
Effective length of query: 539
Effective length of database: 541
Effective search space:   291599
Effective search space used:   291599
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: 41 (21.7 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