GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gly1 in Sinorhizobium meliloti 1021

Align glycine hydroxymethyltransferase (EC 2.1.2.1); low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate SMc01770 SMc01770 serine hydroxymethyltransferase

Query= BRENDA::P0A825
         (417 letters)



>FitnessBrowser__Smeli:SMc01770
          Length = 431

 Score =  497 bits (1280), Expect = e-145
 Identities = 250/418 (59%), Positives = 314/418 (75%), Gaps = 10/418 (2%)

Query: 7   NIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRYYG 66
           ++AD D E++ A+E+E  RQ   IELIASEN  S  V++AQGS +TNKYAEGYPGKRYYG
Sbjct: 13  SLADSDPEIFGAIEKELGRQRHEIELIASENIVSRAVLEAQGSIMTNKYAEGYPGKRYYG 72

Query: 67  GCEYVDIVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLEPGDTVLGMNLAHGGH 126
           GC+YVDI E LAI+RAK+LFG ++ANVQP+SGSQ N AV+ ALL+PGDT +G++L  GGH
Sbjct: 73  GCQYVDIAEALAIERAKKLFGVNFANVQPNSGSQMNQAVFLALLQPGDTFMGLDLNSGGH 132

Query: 127 LTHGSPVNFSGKLYNIVPYGIDATGH-IDYADLEKQAKEHKPKMIIGGFSAYSGVVDWAK 185
           LTHGSPVN SGK +N+V YG+    H +D  ++ ++A+E KPK+II G +AYS + DW +
Sbjct: 133 LTHGSPVNMSGKWFNVVSYGVREDDHLLDMDEVARKAREQKPKLIIAGGTAYSRIWDWKR 192

Query: 186 MREIADSIGAYLFVDMAHVAGLVAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGS 245
            REIAD +GA+L VDMAH+AGLVA G +P+P PH HV TTTTHK+L GPRGG+IL     
Sbjct: 193 FREIADEVGAWLMVDMAHIAGLVAGGQHPSPFPHCHVATTTTHKSLRGPRGGMILT--ND 250

Query: 246 EELYKKLNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVEVFLER 305
           EE+ KK+NSAVFPG QGGPLMHVIA KAVAL EA++P FK Y  QV KNA+ + E     
Sbjct: 251 EEIAKKINSAVFPGLQGGPLMHVIAAKAVALGEALQPSFKDYAAQVVKNARTLAETLKAN 310

Query: 306 GYKVVSGGTDNHLFLVDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTSGIRVG 365
           G  +VSGGTDNHL LVDL  KN TGK A+AALGRA +T NKN +P DP+ PFVTSG+R+G
Sbjct: 311 GLDIVSGGTDNHLMLVDLRKKNATGKRAEAALGRAYVTCNKNGIPFDPEKPFVTSGVRLG 370

Query: 366 TPAITRRGFKEAEAKELAGWMCDVLDSI----NDE---AVIERIKGKVLDICARYPVY 416
            PA T RGFKEAE KE+   + +VLD +    +DE   AV   ++ KV+ +  R+P+Y
Sbjct: 371 APAGTTRGFKEAEFKEVGELIVEVLDGLKAANSDEGNAAVEAGVREKVIKLTDRFPMY 428


Lambda     K      H
   0.316    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: 575
Number of extensions: 23
Number of successful extensions: 3
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: 417
Length of database: 431
Length adjustment: 32
Effective length of query: 385
Effective length of database: 399
Effective search space:   153615
Effective search space used:   153615
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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