GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Azospirillum brasilense Sp245

Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate AZOBR_RS23050 AZOBR_RS23050 decarboxylase

Query= BRENDA::O53554
         (515 letters)



>FitnessBrowser__azobra:AZOBR_RS23050
          Length = 515

 Score =  476 bits (1226), Expect = e-139
 Identities = 270/516 (52%), Positives = 330/516 (63%), Gaps = 11/516 (2%)

Query: 3   GAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYARIA 62
           GA+ L+ TLV  GVD CFANPGTSE+H +AA D++P  R + TLFEGVATGAADGYAR+ 
Sbjct: 3   GAEILVRTLVANGVDTCFANPGTSELHALAAFDSMPGARCVPTLFEGVATGAADGYARMT 62

Query: 63  GRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAGTV 122
            RPAA LLHLGPGL NGLANLHNARRA VPMV +VGDHAT+H+  DAPL SD++ +A  +
Sbjct: 63  DRPAATLLHLGPGLANGLANLHNARRACVPMVNIVGDHATWHRGVDAPLTSDVEGLAKPM 122

Query: 123 SGWVRRTEAAADVGAD-AEAAIAASRSGSQIATLILPADVCWSDGAHAAAGV---PAQAA 178
           S WVR    AA V AD AEA  AA      ++TLILP+D  W D A A   +   PA AA
Sbjct: 123 SAWVRTVPDAASVAADTAEAIRAALTPPCGVSTLILPSDSSWDDTAAAEPIIVEPPAPAA 182

Query: 179 AAPVDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLERGA 238
                +   A  LRSGE  ++L+ G ATR  GL  A RI  ATGA+    T  T +ERGA
Sbjct: 183 PDADALRAAADALRSGERVVVLLNGRATRTEGLALAGRIAAATGAKLYAHTGATRIERGA 242

Query: 239 GIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAEPG 298
           G   VER  Y  +   A L G KH+VL G+  PV FF YP  PS L P  C +H +A PG
Sbjct: 243 GRVTVERFPYPIDLGIAALAGAKHVVLIGSGEPVGFFGYPDKPSRLAPEDCRIHTVAPPG 302

Query: 299 GAADALAA---LADEV-APGTVAPVAGASRPQLPTGDLTSVSAADVVGALLPERAIVVDE 354
             ADALAA   LA+ V   GT  P    + P+  TG LT+ S    + ALLPE AIVVDE
Sbjct: 303 --ADALAALRWLAEAVGCAGTPVPAQPLAPPEPATGALTADSVGQSLAALLPEGAIVVDE 360

Query: 355 SNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTI 414
             +   ++  A AGA AHDWLT+TGGAIG G+P A+GAA+A PDR V+ +++DGS MYT+
Sbjct: 361 GISSSPMVYTACAGARAHDWLTITGGAIGIGMPLALGAAIACPDRKVVTVQADGSGMYTL 420

Query: 415 SGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVKIA 474
             LWSQARE  DV T+I+ N  Y IL+ EL  +G   D GP A +  ++ RP +D+V +A
Sbjct: 421 QALWSQARERADVVTIIFANRRYGILQWELGNLGF-RDMGPNARNCTELGRPDLDWVALA 479

Query: 475 EGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510
            GMGV   + T  E F   L AAFA  GP LI+ V+
Sbjct: 480 RGMGVEGGQATDAESFNRLLTAAFARKGPFLIEAVI 515


Lambda     K      H
   0.318    0.134    0.402 

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: 665
Number of extensions: 32
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: 515
Length of database: 515
Length adjustment: 35
Effective length of query: 480
Effective length of database: 480
Effective search space:   230400
Effective search space used:   230400
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: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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