GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Thermomonospora curvata DSM 43183

Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_012851925.1 TCUR_RS07730 pyridoxal phosphate-dependent aminotransferase

Query= metacyc::MONOMER-21143
         (387 letters)



>NCBI__GCF_000024385.1:WP_012851925.1
          Length = 404

 Score =  164 bits (416), Expect = 3e-45
 Identities = 117/372 (31%), Positives = 189/372 (50%), Gaps = 25/372 (6%)

Query: 18  VLAEAKKLEAQGKPMIHLGLGQP---DFKTPQHVVDAAKKALDEGHHGYVLSNGILECRQ 74
           VL  AK+LEA+G  ++ L +G P    F+ P  ++    + L E H GY  S GIL  R+
Sbjct: 20  VLKRAKELEAEGHQILKLHIGNPAPFGFEAPPEILQDVIRNLPEAH-GYSDSKGILSARR 78

Query: 75  AVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYESMINYT 134
           A+ +  ++   + +D E V +  G    +   +Q     G E++ P P +P++ + +   
Sbjct: 79  AIVQHYEERGFEGLDVEDVYLGNGVSELITMTLQALLNNGDEVLIPAPDYPLWTASVCLG 138

Query: 135 GSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSAIDVLAEGLKK 194
           G TPV Y   E      D + + + IT++T+ L++INPNNPTG+   +  ++ LAE  ++
Sbjct: 139 GGTPVHYLCDEQAGWAPDLDDVEAKITERTKALVIINPNNPTGAVYSRQVLERLAELARR 198

Query: 195 HPHVAILSDEIYSRQIYDGKEMPTFFNY-PDLQDRLIVLDGWSKAYAMTGWRMGWSV--- 250
           H  + I SDEIY R +YDG E  +     PDL    +   G SK Y + G+R GW V   
Sbjct: 199 H-GLIIFSDEIYDRVLYDGAEHISIATLAPDL--LCLTFGGLSKNYRVAGFRSGWVVLSG 255

Query: 251 ---WPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMV---KFDQRRKLIH 304
                E  I  ++ ++ N   C N P+Q A  AAL G   +I+E+++   +  ++R    
Sbjct: 256 PKEHAESYIEGLD-ILANMRLCPNVPAQHAIQAALGG-HQSINELVLPTGRLGEQRDRAW 313

Query: 305 EGLNSLPGVECSLPGGAFYAFPKV---IGTGMNGSEFAKKCMHEAGVAIVPGTAFGKTCQ 361
           + LN +PGV C  P GA Y FP++   +    +  +F  + + +  + +V GT F     
Sbjct: 314 KLLNEIPGVSCVKPQGALYVFPRLDPEVYPIKDDMQFVLELLEDQKLLVVQGTGFNWPAH 373

Query: 362 DYVR---FSYAA 370
           D+ R     YAA
Sbjct: 374 DHFRVVTLQYAA 385


Lambda     K      H
   0.319    0.137    0.414 

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: 29
Number of successful extensions: 6
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: 387
Length of database: 404
Length adjustment: 31
Effective length of query: 356
Effective length of database: 373
Effective search space:   132788
Effective search space used:   132788
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: 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