GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Pseudomonas simiae WCS417

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate GFF3717 PS417_19025 aspartate aminotransferase

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__WCS417:GFF3717
          Length = 401

 Score =  213 bits (542), Expect = 8e-60
 Identities = 140/397 (35%), Positives = 209/397 (52%), Gaps = 24/397 (6%)

Query: 1   MEHLLNPKAREI----EISGIRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDE 56
           M+H L+ +   I     I+     + L AQ  D+++ T+G+PDF TP H+ AAA +A+  
Sbjct: 1   MKHFLSDRVLGIAPSPSIAANALVTELRAQGRDIVNFTVGEPDFDTPAHILAAASQAMHN 60

Query: 57  NVTSYTPNAGYLELRQAVQLYMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEV 116
             T YT   G L LRQA+ L +++  D  Y  + E++   G    I  A    L+ GDEV
Sbjct: 61  GDTHYTSTTGTLALRQAICLKLQQDNDLAYGLD-EVVAGCGGKHVIYHALAATLNRGDEV 119

Query: 117 IMPGPIYPGYEPIINLCGAKPVIVD-TTSHGFKLTARLIEDALTPNTKCVVLPYPSNPTG 175
           I+  P +  Y  I  L  A PVI+    S GFKL+   +E A+T  TK V+L  P+NP+G
Sbjct: 120 IVHTPYWVSYPDIARLNDATPVIIPGDESLGFKLSPDALEQAITARTKWVILNSPNNPSG 179

Query: 176 VTLSEEELKSIAALLKGR-NVFVLSDEIYSELTYDR----PHYSIATYLRDQTIVINGLS 230
              +E EL ++A +L+   +V +++DEIY    Y R    P   +A  L+ +T+++NG S
Sbjct: 180 AVYNETELLALAQVLRRHPHVLIMADEIYEHFIYGRARHVPLTRLAPDLKPRTLIVNGAS 239

Query: 231 KSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQY 290
           K ++MTGWR+GF   P  +   I K+     +C SS+SQ AA+ A T        MRE+Y
Sbjct: 240 KGYAMTGWRLGFGAGPAWLIAAIAKLLSQTTTCPSSLSQAAAVAAFTGDQAPIAAMREEY 299

Query: 291 KKRLDYVYDRLVSM-GLDVVKPSGAFYIFPSIKSF--------GMTSFDFSMA--LLEDA 339
           ++R   +   L  + GL    P GAFY+F ++                D  +   LL D 
Sbjct: 300 QQRRARMLALLADIPGLSCTPPDGAFYVFANVSGLMGKLTPQGDRLDSDTQLVDYLLRDY 359

Query: 340 GVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRLE 376
           G+A V G+++      YVRLSFA S + + EG  RL+
Sbjct: 360 GLATVSGAAYGM--SPYVRLSFASSSEVIEEGCRRLK 394


Lambda     K      H
   0.319    0.135    0.388 

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: 371
Number of extensions: 10
Number of successful extensions: 7
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: 393
Length of database: 401
Length adjustment: 31
Effective length of query: 362
Effective length of database: 370
Effective search space:   133940
Effective search space used:   133940
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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