Aligments for a candidate for ilvH in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Aligments 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis