GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Cupriavidus basilensis 4G11

Align Serine dehydratase-like; L-serine deaminase; L-serine dehydratase/L-threonine deaminase; L-threonine dehydratase; TDH; SDH; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate RR42_RS33880 RR42_RS33880 serine dehydratase

Query= SwissProt::Q8R238
         (329 letters)



>FitnessBrowser__Cup4G11:RR42_RS33880
          Length = 314

 Score =  288 bits (736), Expect = 2e-82
 Identities = 158/306 (51%), Positives = 203/306 (66%), Gaps = 10/306 (3%)

Query: 15  HRVTPLLESWALSQVAGMPVFLKYENVQIAGSFKIRGIGHFCQQMAKRGCRHLVCSSGGN 74
           H VTPLL S + S   G  V+ K E +Q  GSFK RGIGH CQ   + G + LVCSSGGN
Sbjct: 13  HIVTPLLRSTSFSARLGRSVWFKMEALQPPGSFKARGIGHACQTYKEWGAKRLVCSSGGN 72

Query: 75  AGIAAAYSARKLGIPVTIVLPEGTSVQVVRRLEGEGAEVQLTGKVWDEANVKAQELATRD 134
           AGIA AYS R LG+PVT+V+PE TS     R+  EGAE+ + G+ W EAN  A  L  R 
Sbjct: 73  AGIAVAYSGRLLGVPVTVVVPETTSAAARERIAAEGAELVVYGRAWSEANDHALSLM-RP 131

Query: 135 GWVNVSPFDHPLIWEGHASLVRELKESLGTPPGAVVLAVGGGGLLAGVTAGLLEVGWQHV 194
            +  + PFD PL+WEGHA+++ E+  + G  PGAVVL+VGGGGLL GV AGL   GW  V
Sbjct: 132 EYAFIHPFDDPLLWEGHATMIDEVAAA-GVKPGAVVLSVGGGGLLCGVLAGLERNGWHDV 190

Query: 195 PIVAMETRGAHSFNSALQAGRPVTLPDITSVAKSLGAKTVAARTLECAKECEVLSEVVED 254
           P++A ET GA S+ ++L AG  V LP ITS+A SLGA++  A+ LE +K   ++SEVV D
Sbjct: 191 PVIAAETVGADSYAASLAAGAQVELPAITSIATSLGARSPCAKALEWSKVHSIVSEVVTD 250

Query: 255 REAVSAVQRFLDDERMLVEPACGAALAAIYSGILWRLQAEGRLSSALASVVVIVCGGNNI 314
           +EAV A  RFL + R++VEPACGAALAA        L+ +    +A + V+VIVCGG   
Sbjct: 251 KEAVGACLRFLAEHRIVVEPACGAALAA--------LERKPAAVTAASDVLVIVCGGAGA 302

Query: 315 SSQQLQ 320
           +++QLQ
Sbjct: 303 TAEQLQ 308


Lambda     K      H
   0.318    0.134    0.395 

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: 285
Number of extensions: 11
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: 329
Length of database: 314
Length adjustment: 28
Effective length of query: 301
Effective length of database: 286
Effective search space:    86086
Effective search space used:    86086
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: 48 (23.1 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