GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Sinorhizobium meliloti 1021

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate SMc02217 SMc02217 O-succinylhomoserine sulfhydrylase

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



>FitnessBrowser__Smeli:SMc02217
          Length = 394

 Score =  423 bits (1088), Expect = e-123
 Identities = 200/392 (51%), Positives = 282/392 (71%), Gaps = 2/392 (0%)

Query: 11  ITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQN 70
           +++NW+PATQ + GGT RS++GETSEA+FLT G+ YD +  A ARF G+  G  Y+R  +
Sbjct: 1   MSKNWRPATQLVHGGTLRSQYGETSEAIFLTQGFVYDSSEAAEARFKGETDGFIYARYGS 60

Query: 71  PTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQ 130
           PT +M E+R+ +LEGAE  RATASGMAA++AA+LCQ+ AGDH++  RA FGSCRW+ +T 
Sbjct: 61  PTNDMFEKRMCMLEGAEDARATASGMAAVSAAILCQVKAGDHIVAARALFGSCRWVVETL 120

Query: 131 LPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTV 190
            PK+G+E T+VD RD + + DA+RPNTKVFF E+P NPT++V+D+  V  +A + G   V
Sbjct: 121 APKYGVECTLVDGRDLKNWEDAVRPNTKVFFLESPTNPTLEVIDIAGVARLADQIGAKVV 180

Query: 191 VDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGP 250
           VDN FATP  Q+P++ GA VV YSATK +DGQGR L G V   +++++  L  + R+TGP
Sbjct: 181 VDNVFATPLFQKPLELGAHVVVYSATKHIDGQGRCLGGVVLSDKQWVDENLHDYFRHTGP 240

Query: 251 TLSPFNAWVVLKGLETLDLRIQRQSENALKVARFL--EGRVPRVNFPGLPSHPQHNLAMS 308
            +SPFNAW +LKG+ETL LR+++Q+E+A +VA FL  + +V RV +PG   HPQ ++   
Sbjct: 241 AMSPFNAWTLLKGIETLPLRVKQQTESARRVADFLAEQPQVARVIYPGRKDHPQADVIAK 300

Query: 309 QMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRL 368
           QM+    + + EL GG+  A  L +AL +I ISNN+GDS+SL+THPA+TTH  + ++ R 
Sbjct: 301 QMSGGSTLVAFELKGGKEAAFALQNALEIIRISNNLGDSKSLITHPATTTHKNLTDEARA 360

Query: 369 LMGVGEGMLRLNVGLEDPEDLIADLDQALGSV 400
            +G+  G +R + G+ED EDLI D  +AL  V
Sbjct: 361 ELGISAGTVRFSAGIEDSEDLIEDFARALKGV 392


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: 411
Number of extensions: 10
Number of successful extensions: 2
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: 394
Length adjustment: 31
Effective length of query: 371
Effective length of database: 363
Effective search space:   134673
Effective search space used:   134673
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