GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glyA in Pontibacter ramchanderi LP43

Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_101444761.1 BD749_RS11795 serine hydroxymethyltransferase

Query= BRENDA::I7H6W6
         (427 letters)



>NCBI__GCF_002846395.1:WP_101444761.1
          Length = 424

 Score =  468 bits (1205), Expect = e-136
 Identities = 242/429 (56%), Positives = 299/429 (69%), Gaps = 25/429 (5%)

Query: 10  LQTDPTISGMMQKELQRQREHLELIASENFTSPAVMATQGSVLTNKYAEGLPKKRYYGGC 69
           +Q D  I  ++ KE  RQ   +ELIASENF S  VM   GSV+TNKYAEGLP KRYYGGC
Sbjct: 1   MQKDTAIFDLIAKEKARQTHGIELIASENFVSDQVMQAMGSVMTNKYAEGLPGKRYYGGC 60

Query: 70  EFIDEIEQVAIDRAKELFGAASANVQPHSGAQANFAVFLTLLKPGDKIMGMDLSHGGHLT 129
           E +D+ EQ+AIDRAKELFGA   NVQPHSGAQAN AV L +L+PGDKI+G DLSHGGHLT
Sbjct: 61  EIVDQSEQLAIDRAKELFGATWVNVQPHSGAQANSAVMLAVLQPGDKILGFDLSHGGHLT 120

Query: 130 HGSPANVSGKWFEAVHYGVSQETEQLDYDHILEVARQERPKLIICGYSAYPRIINFEKFR 189
           HGSP N SGK ++   YGV QET  +D+D ++E AR+E+PKLIICG SAY R  +++K R
Sbjct: 121 HGSPVNFSGKLYQPSFYGVEQETGLIDFDKVVETARREKPKLIICGASAYSRDWDYKKLR 180

Query: 190 AIADEVGAYLLADIAHIAGLVASGHHPNPVPHCDVVTTTTHKTLRGPRGGLILTRDPELG 249
           A ADEVGA LLADI+H +GL+A G   NP  HC +VTTTTHKTLRGPRGG+I+     +G
Sbjct: 181 AAADEVGALLLADISHPSGLIAKGLLNNPFEHCHIVTTTTHKTLRGPRGGMIM-----MG 235

Query: 250 KKFNK--------------------SVFPGTQGGPLEHVIAGKAVAFGEALKPEFKAYSG 289
           K F                      +VFPGTQGGPLEHVIA KAVA+ EAL  ++  Y  
Sbjct: 236 KDFENPFGLKTPKGEIRMMSSLLDGAVFPGTQGGPLEHVIAAKAVAYYEALSDDYMGYIK 295

Query: 290 QVIANAQAMAQQLQNRGFKIVSGGTDNHLMLVDLRSVNLTGKQADQLVSDVNITANKNTV 349
           QV  NAQAMA     RG+ I+SGGTDNH+ML+DLRS  LTGK A+  +   +IT NKN V
Sbjct: 296 QVQQNAQAMANAFVERGYNIISGGTDNHMMLIDLRSKGLTGKLAENTLVKADITINKNMV 355

Query: 350 PFDPESPFVTSGLRLGSPAMTTRGLGTEDFAEIANIIADRLQNPEDEQVKQACVQRVAAL 409
           PFD +SPFVTSG+R+G+ A+TTRGL   D A I  +I D L N +++   +A  + V + 
Sbjct: 356 PFDDKSPFVTSGMRVGTAAITTRGLKETDMARIVELIDDVLTNNDNDSKIEAVRKEVNSW 415

Query: 410 CERFPLYPH 418
            +++PL+ +
Sbjct: 416 MQQYPLFAY 424


Lambda     K      H
   0.318    0.134    0.393 

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: 546
Number of extensions: 17
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: 427
Length of database: 424
Length adjustment: 32
Effective length of query: 395
Effective length of database: 392
Effective search space:   154840
Effective search space used:   154840
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 (21.7 bits)
S2: 51 (24.3 bits)

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

Links

Downloads

Related tools

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