GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Geobacter metallireducens GS-15

Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_004514090.1 GMET_RS03510 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::O31631
         (373 letters)



>NCBI__GCF_000012925.1:WP_004514090.1
          Length = 378

 Score =  324 bits (831), Expect = 2e-93
 Identities = 161/372 (43%), Positives = 236/372 (63%), Gaps = 16/372 (4%)

Query: 7   TKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLEN 66
           T++   G+  D  TG VS PIY ++ +R   +     +DY R+ NPTR+ +E+ IA LE 
Sbjct: 5   TRIIHTGHDIDPTTGAVSIPIYQTSTFRQESVDHFGKYDYARSDNPTREALEETIAQLEG 64

Query: 67  GARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFSDE 126
           G RG A++SGMAAI +++ LF  GD L+V  D+YGGT+R+    + + G+T  + D +D 
Sbjct: 65  GTRGFAYASGMAAISSVLLLFSPGDHLVVCEDVYGGTFRVLTQLFSRLGITSTFVDATDL 124

Query: 127 DCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLEL 186
           D + +   P TK +F+E+P+NPL++  D+E  ARI +E G + +VDNTF TP LQRPLE+
Sbjct: 125 DAIAAAFRPETKGLFLESPSNPLLKITDLEGAARIARERGAITLVDNTFMTPYLQRPLEV 184

Query: 187 GADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMKT 246
           G DIV+HS TK+L GH+D++ G  VVKD  LG+ +   QNA GA+L P DSWL++RG+KT
Sbjct: 185 GCDIVLHSGTKFLNGHSDVICGFAVVKDPELGKRIRFIQNAFGAILGPQDSWLVLRGLKT 244

Query: 247 LSLRMRQHQANAQELAAFLEEQEEISDVLYP----------------GKGGMLSFRLQKE 290
           L +RM + Q +A  +A++L  ++ ++ VLYP                G G +LSF L   
Sbjct: 245 LRVRMEESQRSATRIASWLAGEKRVTRVLYPGLPSHPGHAIHARQSSGPGAVLSFALDSL 304

Query: 291 EWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGIEH 350
           E     L+ +K   FA SLGGVES I+YPA  +H  +P E R A G+ + L+R SVG+E 
Sbjct: 305 EVTRRLLEGMKLAAFAVSLGGVESIISYPARMSHAAMPPEERAARGIGDTLVRLSVGLEE 364

Query: 351 AEDLKEDLKQAL 362
           A+DL  ++ + +
Sbjct: 365 ADDLIAEMDRLI 376


Lambda     K      H
   0.319    0.135    0.392 

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: 349
Number of extensions: 9
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: 373
Length of database: 378
Length adjustment: 30
Effective length of query: 343
Effective length of database: 348
Effective search space:   119364
Effective search space used:   119364
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 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