GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argJ in Rhizorhabdus wittichii RW1

Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_012048893.1 SWIT_RS13595 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ

Query= BRENDA::Q92MJ1
         (413 letters)



>NCBI__GCF_000016765.1:WP_012048893.1
          Length = 407

 Score =  424 bits (1089), Expect = e-123
 Identities = 232/408 (56%), Positives = 279/408 (68%), Gaps = 4/408 (0%)

Query: 6   SPLAPKTFAEMPALRGVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCPSAPVD 65
           SPLAP  F ++P + G R+A A AG K  +R D+    FD    VAGV T S+CPS  V+
Sbjct: 4   SPLAPAAFPDLPPIAGARVAVARAGYKRWDRADLTYAAFDEGTVVAGVTTTSRCPSPEVE 63

Query: 66  HCRQNLPGGIARAVVVNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFLASTGVIG 125
            CR  LP G ARA+VVN+GN+NAFTG +GR A        A A+GC  ++VF+ASTGVIG
Sbjct: 64  WCRAALPLGQARALVVNAGNSNAFTGNRGRAAVEAITARVAGAIGCRPSDVFVASTGVIG 123

Query: 126 EPLDATKFAGVLDKLAASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVKVAINGIAKG 185
            PL   K    +D +   A +  W EAA  IMTTDT+ K A  SA +GG +V + GI KG
Sbjct: 124 VPLPIDKAEAGIDAVLR-APEASWEEAAATIMTTDTFAKAARASAMVGGARVELVGIVKG 182

Query: 186 AGMIAPDMATMLSFVVTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSDTLMLFATGA 245
           +GMIAPDMATML FV TDA IAP  LQA+L      +F+ +TVD DTSTSDT++ FATG 
Sbjct: 183 SGMIAPDMATMLGFVFTDAAIAPELLQAMLNRANARSFSCITVDGDTSTSDTVLAFATGK 242

Query: 246 AAGDGQAKVEDAADPRLDGFRAALDDLLRDLALQVVRDGEGARKMVEVTVEGAENDAAAK 305
           A   G A++E   DP  D   AAL+ +  +LA  VVRDGEGA K + VTVEGAE+DA+A 
Sbjct: 243 A---GHARLETMDDPGADALEAALNAVCLELAQLVVRDGEGASKFIAVTVEGAESDASAH 299

Query: 306 RIALSIANSPLVKTAVAGEDANWGRVVMAVGKSGEMAERDRLAIWFGDIRVAVEGERDPA 365
           RIALSIANSPLVKTA+AGEDANWGRVVMAVGK+GE AERDRL+I FG  +VA  G     
Sbjct: 300 RIALSIANSPLVKTAIAGEDANWGRVVMAVGKAGEPAERDRLSIRFGATQVATGGLAVEG 359

Query: 366 YSEAAATAVMQGETIPIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413
           Y EA   A ++G  I I VDIGLG+GRATV+TCDLT  Y+ IN DYRS
Sbjct: 360 YDEAPVAAHLKGREIEIGVDIGLGNGRATVWTCDLTHGYISINADYRS 407


Lambda     K      H
   0.316    0.130    0.365 

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: 414
Number of extensions: 11
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: 413
Length of database: 407
Length adjustment: 31
Effective length of query: 382
Effective length of database: 376
Effective search space:   143632
Effective search space used:   143632
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: 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