GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Sphingomonas indica Dd16

Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_085218863.1 B9N75_RS11115 thiamine pyrophosphate-binding protein

Query= curated2:Q7U5G1
         (617 letters)



>NCBI__GCF_900177405.1:WP_085218863.1
          Length = 552

 Score =  219 bits (559), Expect = 2e-61
 Identities = 177/533 (33%), Positives = 249/533 (46%), Gaps = 57/533 (10%)

Query: 19  QTISGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAA 78
           Q  +G   L+D L   G D IF  PG + L   DALH   +   +  ++ R E    + A
Sbjct: 3   QLRTGGRILIDNLLAQGCDRIFCVPGESYLAALDALHDTPA---IDLVVCRQEGGVAYMA 59

Query: 79  DAYARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDI 138
           +A  + TG+ GV F T GPGATN   G+  A+ DS PMV++ G V R     + FQE D 
Sbjct: 60  EADGKMTGRPGVAFVTRGPGATNASVGVHVARQDSTPMVLLIGDVARGDRDREGFQEVDF 119

Query: 139 FGITLPIVKHSWVVR--DPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVE 196
             +  P+ K  WV R  D   +   VA+A+  A +GRPGPV++ +P+D+ +++   V   
Sbjct: 120 LTMFAPLAK--WVARIEDARRIPEYVARAWRTATAGRPGPVVLVLPEDMLRDEVEAVDRP 177

Query: 197 PGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLP 256
               I     Q   PL  AV + + L++ A  PL  VGGG   + A    R  AER  LP
Sbjct: 178 ANPCIA----QAADPL--AVGSLMTLLQDACAPLAIVGGGGWCSGAGHYFRDFAERIGLP 231

Query: 257 VTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKLDTFA- 315
           V T    + A   +  +  G LG          V   DLL+ VGAR  +  T      A 
Sbjct: 232 VATAFRRQDAIGADSPVYAGNLGYGPNPKLVERVKNADLLLVVGARLGEATTDGYTLIAP 291

Query: 316 --PRARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVE-------ISLQRTAEPRTAA 366
             P   +VH   DP E+G   + D+ +  D+    A +V        IS    AE     
Sbjct: 292 DHPGQTLVHVHPDPNELGSVYRTDLPICADM-REFAELVADWEEQEVISFDAGAEAH-RE 349

Query: 367 WLERINTWKDRYPLTIPPAEGAIYPQE---VLLAVRDLAP-DAIVTTDVGQ-----HQMW 417
           WLE    W      ++P A G   P +   V+ A+RD  P D I+    G      H+ W
Sbjct: 350 WLE----W------SMPRATGG--PLDLGLVVEAMRDALPADTIICNGAGNFSGWWHRFW 397

Query: 418 --AAQHLRNGPRGWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGT 475
             AA   +  P         G+MG+G PAA+ A +  PDR VV +AGD   LMN QEL T
Sbjct: 398 PYAALPSQLAPTN-------GSMGYGPPAAVAAALRFPDRTVVAVAGDGDFLMNGQELAT 450

Query: 476 LAAYGLPVKVVIVNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFG 528
              +   + V++++N   G +R  QE  Y ER   + ++N  PDF   A++FG
Sbjct: 451 AMRHDTDMLVLVIDNASYGTIRMHQEREYPERVVGTGLVN--PDFAQFAKAFG 501


Lambda     K      H
   0.320    0.136    0.414 

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: 927
Number of extensions: 47
Number of successful extensions: 6
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: 617
Length of database: 552
Length adjustment: 36
Effective length of query: 581
Effective length of database: 516
Effective search space:   299796
Effective search space used:   299796
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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