GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Pseudomonas stutzeri RCH2

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate GFF2528 Psest_2578 O-succinylhomoserine sulfhydrylase

Query= reanno::Korea:Ga0059261_3194
         (402 letters)



>FitnessBrowser__psRCH2:GFF2528
          Length = 403

 Score =  335 bits (859), Expect = 1e-96
 Identities = 178/384 (46%), Positives = 242/384 (63%), Gaps = 3/384 (0%)

Query: 19  TQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQ 78
           T A+R G  R+  GE  E LF TS Y +  A DAAARF+GD  G  YSR  NPTV   E+
Sbjct: 21  TLAVRAGQRRTPEGEHGEPLFFTSSYVFRSAADAAARFAGDVPGNVYSRYTNPTVRAFEE 80

Query: 79  RIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIET 138
           RIA LEGAE   ATASGMAA+ A ++   +AGDH++  R+ FG+   L +  L +FG++ 
Sbjct: 81  RIAALEGAEQAVATASGMAAILATVMSLCAAGDHVLVSRSVFGATVSLFEKYLKRFGVQV 140

Query: 139 TVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATP 198
             V   D   +  A + NTK+ F E+P+NP  ++VD+ A+  +   +G +  VDN F TP
Sbjct: 141 DYVPLTDFSAWESAFQENTKLVFVESPSNPLAELVDIAALAKLCHAKGAMLAVDNCFCTP 200

Query: 199 ALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAW 258
            LQ+P+  GAD+V +SATK +DGQGR L G V G  E +   L+ F R  GPTLSPFNAW
Sbjct: 201 VLQQPLALGADIVIHSATKYIDGQGRCLGGVVAGRSEQMKE-LVGFLRTAGPTLSPFNAW 259

Query: 259 VVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAAGPI 316
           V LKGLETL LR+Q    +A ++A +LE +  + RV + GLPSHPQH LA  Q    G +
Sbjct: 260 VFLKGLETLRLRMQAHCASAQELAEWLEQQPGIERVYYAGLPSHPQHELAKRQQKGFGAV 319

Query: 317 FSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGM 376
            S E+ GG+  A   +DA  LI I+ N+GDS++ +THP STTH  ++ + R   G+ + +
Sbjct: 320 VSFEVAGGKEAAWRFIDATRLISITANLGDSKTTITHPGSTTHGRLSAEDRATAGIRDSL 379

Query: 377 LRLNVGLEDPEDLIADLDQALGSV 400
           +R+ VGLED  DL ADL + L ++
Sbjct: 380 IRVAVGLEDVADLKADLARGLAAL 403


Lambda     K      H
   0.319    0.134    0.396 

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: 409
Number of extensions: 14
Number of successful extensions: 3
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: 402
Length of database: 403
Length adjustment: 31
Effective length of query: 371
Effective length of database: 372
Effective search space:   138012
Effective search space used:   138012
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: 50 (23.9 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