GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Desulfotalea psychrophila LSv54

Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_011190179.1 DP_RS14870 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::Q56232
         (385 letters)



>NCBI__GCF_000025945.1:WP_011190179.1
          Length = 395

 Score =  168 bits (426), Expect = 2e-46
 Identities = 115/357 (32%), Positives = 175/357 (49%), Gaps = 16/357 (4%)

Query: 39  GEPDFDTPEHVKEAARRALAQ---GKTKYAPPAGIPELREALAEKFRRENGLSVTPEETI 95
           G PD   P    +   +  A    G   Y P  G   +REA+A +  +E G+ V   + +
Sbjct: 42  GNPDAPPPAQFDQVLAKIAADNGPGTHSYMPNGGHLWVREAVAGQMAKEQGVKVVASDML 101

Query: 96  VTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVVEVETLPEEGFVPDPE 155
           ++ G    +  + +++L+PGDEVI L+PY+V Y   V   GG    V+T  +E F PD  
Sbjct: 102 LSCGAAGGINVIMKSLLNPGDEVIFLAPYFVEYDFYVDNHGGKSRVVQT--DENFNPDMA 159

Query: 156 RVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVE------HDFYLVSDEIYEHL 209
            +R AI+ +TKA+++NSPNNPTG +Y KE+L  L  L  E         YL+SDE Y  +
Sbjct: 160 AIREAISEKTKAIIINSPNNPTGQIYSKEILAELGLLLTEMGEKFGSTIYLISDEPYRKI 219

Query: 210 LYEGEHFSPGRVAPEHTLTVNGAAKAFAMTGWRIGYACGPKEVIKAMASVSSQSTTSPDT 269
            Y+G        A  +++ V+  +K  ++ G RIGY      + +    VS+   T  + 
Sbjct: 220 TYDGIEVPSIFAAYSNSIIVSSYSKDLSLPGERIGYVAVHPGISEKAELVSAM--TLANR 277

Query: 270 IAQWATLEALTNQE-ASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTS 328
           I  +    AL  +  A    + +  E Y RRR+   + LT  G   V P GAFY+    S
Sbjct: 278 ILGFVNAPALMQRVIAELQGISVDNERYARRREAFCQILTEAGFDFVPPKGAFYI-FPKS 336

Query: 329 PIAPDEVRAAERLLEAGVAVVPGTDFAAFGHVRLSYATSEENLRKALERFARVLGRA 385
           PI  D+V     L E  +  VPG  F A G++RL++   +E +  +   F R   +A
Sbjct: 337 PI-EDDVAFCAILQEEKILAVPGRGFGAPGYIRLAFCVPDETIAGSAAAFKRAYQKA 392


Lambda     K      H
   0.317    0.133    0.379 

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: 377
Number of extensions: 14
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: 385
Length of database: 395
Length adjustment: 31
Effective length of query: 354
Effective length of database: 364
Effective search space:   128856
Effective search space used:   128856
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 (21.7 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