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_152617477.1 BS73_RS01920 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000744815.1:WP_152617477.1
          Length = 572

 Score =  327 bits (838), Expect = 8e-94
 Identities = 221/562 (39%), Positives = 297/562 (52%), Gaps = 27/562 (4%)

Query: 31  AAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKEGVFSAGGYPLEFG 90
           A  R   RA+G+ DED  KP+I V ++ +E+  C   LD +A  VKEGV +AGG P E  
Sbjct: 14  ATRRSQWRALGLSDEDMLKPKIAVVNTSSELAVCFSHLDGVAARVKEGVRAAGGLPFEVR 73

Query: 91  TISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDKSLPGMLMAAAR 150
           T + SD I     G  + L +R++I + +EV ++  +LDG + LA CDK+ PG LMAA R
Sbjct: 74  TTAPSDFIHSAGHGGGYILSARDLIVNDIEVGVEGAQLDGMICLASCDKTAPGQLMAAGR 133

Query: 151 LDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSRADVDAIERAICPG 210
           LD+  + L  G   P  +   +  + +   + A    GA     ++    DA+      G
Sbjct: 134 LDIPTLLLACG-YQPSGSYRGEHCDIEDVFLHACGTPGAELTAELTEMSEDAVR-----G 187

Query: 211 EGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVELLRRGITARD 270
            G C GM TAN+M   AEALGM+LPGS    A        A R+   +VEL+R  +  R 
Sbjct: 188 PGVCAGMGTANSMHIVAEALGMALPGSTPVAADSPAMWREADRAAARIVELVREDVRPRA 247

Query: 271 ILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALS-LQDFSRIGSGVPHLADVKPF 329
           +LT  AF NA+ V ++ G S N V HL A+A EA V L  L  F+  G+  P L+ V+P 
Sbjct: 248 VLTAAAFRNAVRVALSVGASINTVKHLQAVAAEAEVDLDVLGLFAEYGAVTPLLSAVRPN 307

Query: 330 GRHVMSDVDHIGGVPVVMK--ALLDAGLLHGDCLTVTGHTMAENLAAITPPDP------- 380
           G H +   D  GG   VM+  A LD GLL  D  TV+GH + ENLA     DP       
Sbjct: 308 GPHTIEQFDAAGGARAVMRRLAALD-GLLDLDAPTVSGHIVGENLAGAEATDPATDRDTD 366

Query: 381 -----DGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSD---VFEGTARVFDGE 432
                  +V+R    P      I IL GSL P G +VK +  D +    F G AR F+ +
Sbjct: 367 TEADAHAEVIRPADRPFSREPLIVILRGSLCPLGGIVKLS-VDHERPTGFSGPARCFERQ 425

Query: 433 RAALDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSG 492
             A+ AL  G I  GD VV+R  GP+G PGM     I  A+  AGL   V ++TDG+ SG
Sbjct: 426 EDAVAALAAGAIGAGDVVVLRGLGPRGRPGMGMASQIVFALDRAGLTGRVAVVTDGQLSG 485

Query: 493 -GTTGLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPP 551
               G+ VG + PEA DGGP+AL+R+GDRIR+DV GR  ++  +PAE   R+ +    P 
Sbjct: 486 LVNRGIVVGEVRPEAADGGPLALVRDGDRIRVDVPGRGCELDVEPAELERRRAERPTLPE 545

Query: 552 RYTTGVLSKYVKLVSSAAVGAV 573
               G LS Y + V   A GAV
Sbjct: 546 YGERGWLSVYRRTVQPLADGAV 567


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: 978
Number of extensions: 59
Number of successful extensions: 7
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: 575
Length of database: 572
Length adjustment: 36
Effective length of query: 539
Effective length of database: 536
Effective search space:   288904
Effective search space used:   288904
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