GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Ruegeria conchae TW15

Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_010439268.1 G7G_RS0105370 hypothetical protein

Query= BRENDA::O06335
         (552 letters)



>NCBI__GCF_000192475.1:WP_010439268.1
          Length = 524

 Score =  135 bits (340), Expect = 4e-36
 Identities = 158/562 (28%), Positives = 237/562 (42%), Gaps = 64/562 (11%)

Query: 3   VGDHLVARMRAAGISVVCGLPTSRLDSLLVRLSRDAGFQIVLARHEGGAGYLADGFARAS 62
           +G  +   ++  G+ V+ G+P    +  + R   +AG   VLARHE GAG++ADG+ARAS
Sbjct: 5   LGAQISHMLKDRGVDVIFGIPGVH-NQEMYRGIEEAGITHVLARHEQGAGFMADGYARAS 63

Query: 63  GKSAAVFV-AGPGATNVISAVANASVNQVPMLILTG---EVAVGEFGLHSQQDTSDDGLG 118
           GK    +V  GPG  N+++ +  A  + VPML+L+    +V      LH  +D      G
Sbjct: 64  GKPGVAYVITGPGLCNIMTPMGQAYSDSVPMLVLSSCLDDVQSRRGQLHQMKDQR----G 119

Query: 119 LGATFRRFCRCSVSIESIANARSKIDSAFRALASIPRGPVHIALP-RDLVDERLPAHQLG 177
              T   +   S   +   +    ++ AF         P HI +P   L  E  PA    
Sbjct: 120 AADTVADW---SCQADDAQSTYLLVERAFEDFELSRPRPKHIQIPIAQLEAEAEPAPFPN 176

Query: 178 TAAAGLGGLRTLAPCGPDVADEVIGRLDRSRAPMLVLGNGCRLDGIGEQIVAFCEKAGLP 237
             A     LRT A   PDVA  V+  L+ ++ P+ +LG G R   +  QI+    + G  
Sbjct: 177 QPA-----LRTKA-LPPDVA-PVLSLLNIAQRPLFILGGGSR-SNLWRQILT---ELGAA 225

Query: 238 FATTPNGRGIVAETHPLSLGVLGIFGDGRADEYLFDTPCDLLIAVGVSFGGLVTRSFSPR 297
             TT  GRG+V   +PL  G + +   G A+        DL++ VG   G +        
Sbjct: 226 CFTTFAGRGLVGANYPLDFGSM-LPRPGSAEVI---ASADLVVVVGAELGEV------DL 275

Query: 298 WR---GLKADVVHVDPDPSAVGRFVATSLGITTSGRAFVNAL-----------NCGRPPR 343
           WR   G  A +V VD DP  +      ++ I   G +F  AL              +   
Sbjct: 276 WRDRLGHSAQLVRVDIDPEVLSDHHRATVKIQADGESFAYALWQSVEKVQPAGGWSQDEV 335

Query: 344 FCRRVGVRPPAPAALPGTPQARGESIHPLELMHELDRELAPNATICADVGTCISWTFRGI 403
              R   R    A LPG  Q           + +  RE  P  T+     T  ++  + I
Sbjct: 336 SEARARWRAEINAELPGIVQ-----------VSDALREAMPVETMIYSDMTQFAYVSKEI 384

Query: 404 -PVRRPGRFFATVDFSPMGCGIAGAIGVALARPEEHVICIAGDGAFLMHGTEISTAVAHG 462
             +  P  +     F  +G  +   IG A+AR  +    IAGD  F     E+  AV  G
Sbjct: 385 WDMHYPYHWHHPTGFGTLGYALPAGIGGAMARRGKPTAVIAGDYGFHYTMQELGVAVELG 444

Query: 463 IRVTWAVLNDGQMSASAGPVSGRMDPSPVARIGAN-DLAAMARALGAEGIRVDTRCELRA 521
           + +   + ++G++ A    +  R   +P A I  N D   +A A GA         E++A
Sbjct: 445 LPLPIILWDNGKLKAIEDSMV-RSQIAPNAVIARNPDFCKLAEAFGARSAEPGNLDEMQA 503

Query: 522 GVQKALAATGPCVLDIAIDPEI 543
            V+KA  A GP +  I I PEI
Sbjct: 504 AVRKAFTANGPTL--IRITPEI 523


Lambda     K      H
   0.322    0.139    0.425 

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: 674
Number of extensions: 36
Number of successful extensions: 4
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: 552
Length of database: 524
Length adjustment: 35
Effective length of query: 517
Effective length of database: 489
Effective search space:   252813
Effective search space used:   252813
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 (21.9 bits)
S2: 52 (24.6 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