GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glyA in Azorhizobium caulinodans ORS 571

Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate WP_043879456.1 AZC_RS15745 serine hydroxymethyltransferase

Query= metacyc::MONOMER-4244
         (434 letters)



>NCBI__GCF_000010525.1:WP_043879456.1
          Length = 424

 Score =  592 bits (1525), Expect = e-174
 Identities = 286/410 (69%), Positives = 341/410 (83%)

Query: 24  DPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSVLTNKYAEGYPGKRYYGGCQYV 83
           D  +F AI +E GRQ+ +IELIASENIVS+AVL A GSVLTNKYAEG PGKRYYGGC++V
Sbjct: 12  DRAVFDAIARELGRQRDQIELIASENIVSEAVLAAQGSVLTNKYAEGLPGKRYYGGCEHV 71

Query: 84  DIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALAQPGDTILGLSLAAGGHLTHGA 143
           D+VE+IAIDRAK+LF C FANVQP+SG+QAN  V  AL QPGDT+LG+SLAAGGHLTHGA
Sbjct: 72  DVVEEIAIDRAKQLFGCGFANVQPHSGAQANAAVLMALLQPGDTLLGMSLAAGGHLTHGA 131

Query: 144 PVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRIIIAGGSAYPRKIDFAAFRAIA 203
           P   SGKWF AV Y V P++ LID DEV +LA  H+P++IIAGGS+YPR IDFA FRAIA
Sbjct: 132 PPTLSGKWFNAVGYGVSPETALIDYDEVERLAHAHRPKLIIAGGSSYPRIIDFARFRAIA 191

Query: 204 DEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHKTLRGPRGGMILTNDADIAKKI 263
           D VGA  +VD AH+AGL+ AG  PSPFPHAH+VTTTTHKTLRGPRGG+ILTND  +AKK+
Sbjct: 192 DAVGAHLMVDAAHYAGLIVAGAYPSPFPHAHIVTTTTHKTLRGPRGGLILTNDEALAKKL 251

Query: 264 NSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQVMDNARALGEVLVQNGFALVSG 323
           NSA+FPG+QGGPLMHVIA KAVAFGEAL+PDF+ Y  QV+ NARAL   L + G A+VSG
Sbjct: 252 NSAVFPGLQGGPLMHVIAAKAVAFGEALQPDFRTYALQVVSNARALAARLAEKGAAIVSG 311

Query: 324 GTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPFDPEKPMVTSGIRLGSPAGTTR 383
           GTD+H+VLVDLRP  +TG  AE AL RA +TCNKNGIPFDP+KP VTSGIRLG+PAGTTR
Sbjct: 312 GTDSHMVLVDLRPFNVTGKAAEIALERAGLTCNKNGIPFDPQKPAVTSGIRLGTPAGTTR 371

Query: 384 GFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVKAKAIALCDRFPIY 433
           GFG+ EF+++G +I+EVL G+A++G++GN   EA V+ +  ALC RFP+Y
Sbjct: 372 GFGLGEFEQVGDMIAEVLKGLAQSGDEGNSLTEARVRGEVEALCRRFPLY 421


Lambda     K      H
   0.319    0.136    0.396 

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: 613
Number of extensions: 24
Number of successful extensions: 1
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: 434
Length of database: 424
Length adjustment: 32
Effective length of query: 402
Effective length of database: 392
Effective search space:   157584
Effective search space used:   157584
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: 51 (24.3 bits)

This GapMind analysis is from Jul 25 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