GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Pseudomonas stutzeri RCH2

Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate GFF2541 Psest_2591 3-isopropylmalate dehydratase, large subunit

Query= curated2:O27668
         (428 letters)



>FitnessBrowser__psRCH2:GFF2541
          Length = 475

 Score =  194 bits (493), Expect = 5e-54
 Identities = 141/444 (31%), Positives = 212/444 (47%), Gaps = 65/444 (14%)

Query: 30  VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPANTIGAAE--FQRVT 87
           +D  + H+ TSP      R +A+R    + W  +  +   DHNVP  T G  +   + + 
Sbjct: 28  IDRHILHEVTSPQAFEGLR-LANR----KPWRIDANIATPDHNVPT-TKGERQGGLEAIA 81

Query: 88  REFAREQ-----------GIVNIFQNAA--GICHQVLPERGFVRPGMVIVGADSHTCTYG 134
            E +R Q           GI+    N    GI H + PE+G   PGM +V  DSHT T+G
Sbjct: 82  DEVSRIQVQTLDENCDDFGILEFKMNDVRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHG 141

Query: 135 AFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDG 194
           AFGA A G+G +++  V AT        + M++ V G+    V AKD++L +IG+IG  G
Sbjct: 142 AFGALAHGIGTSEVEHVLATQCLVAKKMKNMQVRVEGKLPFGVTAKDIVLAVIGKIGTAG 201

Query: 195 ATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRAR--------- 245
               ++EF G  I  + + GRMTICNM++E GA+ G++  + +T+ YV  R         
Sbjct: 202 GNGHALEFAGSAIRDLSMEGRMTICNMSIEAGARVGMVAVDEKTIAYVEGRPFAPKGDDW 261

Query: 246 --TGREFRVYSSDEDSQYLEDHHFDVSDLEPQVA--------------CPDDVDNVYPVH 289
                 ++   SD+D+ +         D++PQV+               PD      PV 
Sbjct: 262 DKAVELWQGLVSDDDAVFDTVVELKAEDIKPQVSWGTSPEMVLAVDQKVPDPAVEADPVK 321

Query: 290 R-----------------VEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVR-FI 331
           R                 +    +D  F+GSCTN R EDL+ AAEV   R+V  +V+  +
Sbjct: 322 RDSIMRALKYMGLNANQPITEIKLDRVFIGSCTNSRIEDLRAAAEVAKGRKVAANVKQAL 381

Query: 332 VSPASREIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRG 391
           V P S  +  +A  +G+ + F+ AG     PGC  CL  +   L  GE   +T+NRNF G
Sbjct: 382 VVPGSGLVKQQAEAEGLDKIFVEAGFEWREPGCSMCLAMNPDKLGSGEHCASTSNRNFEG 441

Query: 392 RMGDPASSVYLANPAVVAESAIEG 415
           R G      +L +PA+ A +A+ G
Sbjct: 442 RQG-AGGRTHLVSPAMAAAAAVTG 464


Lambda     K      H
   0.320    0.137    0.408 

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: 504
Number of extensions: 27
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: 428
Length of database: 475
Length adjustment: 33
Effective length of query: 395
Effective length of database: 442
Effective search space:   174590
Effective search space used:   174590
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: 51 (24.3 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