GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Phyllobacterium endophyticum PEPV15

Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate WP_106715050.1 CU100_RS02980 hypothetical protein

Query= SwissProt::P06106
         (444 letters)



>NCBI__GCF_003010935.1:WP_106715050.1
          Length = 394

 Score =  159 bits (402), Expect = 1e-43
 Identities = 116/410 (28%), Positives = 188/410 (45%), Gaps = 51/410 (12%)

Query: 28  PIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSNVLEERIAALEGGAAALAVSSGQ 87
           PI+ T+ + +++ +    +F      Y+YSR  NPT    E   A LEG       S+G 
Sbjct: 33  PIFQTSLFTYDSYEAMEDVFAGRSRNYIYSRGDNPTVREFELLTARLEGAEDGRGFSNGT 92

Query: 88  AAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRFGIEARFVEGDNPEEFEKVFDER 147
           AA T  I  L   GD +V+  +LY   Y  F     RFG+   FV+  N +E        
Sbjct: 93  AAITATILSLVEAGDRVVAVRHLYNDIYRLFVKLLARFGVAVDFVDPSNHDEVRAAL-PG 151

Query: 148 TKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNTFGAGGYFCQPIKYGADIVTHSA 207
            K +YLE   +  + + D E + A+A ++G+  V+DN++ A   F +PI++G D+V H+A
Sbjct: 152 AKLLYLENPTSMVFELQDIEALAAMAKEYGVVSVIDNSW-ATPLFQKPIQHGVDLVIHAA 210

Query: 208 TKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAEGYHGTIYNEAYGNLAYIVHVRT 267
           +K++GGH  T+ G++V                                 G    I  + +
Sbjct: 211 SKYLGGHSDTVAGVVV---------------------------------GPRDLIAKINS 237

Query: 268 ELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALKLAKWLEQSPYVSWVSYPGLASH 327
                +G  ++PF ++LLL+G+ TL +R + H  N L LA+ L+Q P +S V +P  + H
Sbjct: 238 TTYPYIGAKLSPFEAWLLLRGMRTLKVRLKEHMHNGLVLARHLQQHPDISLVRHPAFSDH 297

Query: 328 SHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLSGAQVVDNLKLASNLANVGDAKT 387
                 KK L+ GF G+ +F +   P+ D          A+ V+ L+      + G  +T
Sbjct: 298 ----QGKKTLT-GFSGLFAFDLS--PDVDV---------ARFVNALRHIRLGVSWGGPET 341

Query: 388 LVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFIDDIIADFQQSFET 437
           LV+               +  GV    IR +VG+E  + I  D QQ+  +
Sbjct: 342 LVVPAKAALQIPDRMTSFVRFGVNPQTIRFAVGLEEPEIIWNDLQQALHS 391


Lambda     K      H
   0.317    0.136    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: 430
Number of extensions: 21
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 444
Length of database: 394
Length adjustment: 32
Effective length of query: 412
Effective length of database: 362
Effective search space:   149144
Effective search space used:   149144
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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