GapMind for Amino acid biosynthesis

 

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

Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_004514768.1 GMET_RS12040 homocysteine synthase

Query= SwissProt::Q9WZY4
         (430 letters)



>NCBI__GCF_000012925.1:WP_004514768.1
          Length = 428

 Score =  547 bits (1410), Expect = e-160
 Identities = 275/425 (64%), Positives = 328/425 (77%), Gaps = 3/425 (0%)

Query: 5   KYGYNTRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGNP 64
           K  ++T ALHAG EP +  T SRAVPIYQT SY F+ S+HAA LF L+E G IYTR+ NP
Sbjct: 5   KISFDTLALHAGQEP-DPTTLSRAVPIYQTASYAFKSSEHAANLFGLKEFGNIYTRLMNP 63

Query: 65  TVSVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHTL 124
           T  VLE+R+A L+ GVGALAVASGQAAITYA+LNIA  G  IVS S LYGGTYNLF +TL
Sbjct: 64  TSDVLEKRLAELDGGVGALAVASGQAAITYAVLNIAQAGQNIVSTSYLYGGTYNLFHYTL 123

Query: 125 YKKSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLI 184
             K GI VKFVD +DP+N+  AI +KT+ VY E++GNP   V DFEAIA IAH  G+P +
Sbjct: 124 -PKLGITVKFVDTSDPENVRRAIDDKTRLVYTESVGNPKNNVDDFEAIARIAHEAGIPFV 182

Query: 185 VDNTVAP-YIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNGKFPELVEPD 243
           VDNTV   Y+F+P EHGADIVVYS TKFIGGHGTSIGG +VD GKF W NG+FPE+ EPD
Sbjct: 183 VDNTVTTSYLFKPLEHGADIVVYSLTKFIGGHGTSIGGAVVDGGKFPWNNGRFPEMTEPD 242

Query: 244 PSYHGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENAL 303
           PSYHG+ Y E     +YI K R  LLRD+G+C+SPFN+FLF+ GLETL +RM +H ENA 
Sbjct: 243 PSYHGLCYWEALGNLSYILKMRITLLRDMGACISPFNSFLFLQGLETLPVRMARHVENAR 302

Query: 304 KIVEFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSLT 363
            + ++L+ HP VSWVNYP    +K   NA KYL +G GAI+ FG+ GG EAG++FIDS  
Sbjct: 303 AVAQWLEKHPLVSWVNYPGLASHKDHGNARKYLPKGEGAIIGFGINGGLEAGRRFIDSAK 362

Query: 364 LISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQA 423
           L+SHLANIGDA++L IHPASTTHQQL+EEEQL +GVT D IRLS+GIE+V DIIAD+DQA
Sbjct: 363 LLSHLANIGDAKSLVIHPASTTHQQLSEEEQLASGVTQDYIRLSIGIEEVADIIADIDQA 422

Query: 424 LRKSQ 428
           L  SQ
Sbjct: 423 LAASQ 427


Lambda     K      H
   0.317    0.136    0.398 

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: 610
Number of extensions: 26
Number of successful extensions: 5
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: 430
Length of database: 428
Length adjustment: 32
Effective length of query: 398
Effective length of database: 396
Effective search space:   157608
Effective search space used:   157608
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: 51 (24.3 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