GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Phyllobacterium endophyticum PEPV15

Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_106717290.1 CU100_RS14195 histidinol-phosphate transaminase

Query= metacyc::BSU22620-MONOMER
         (360 letters)



>NCBI__GCF_003010935.1:WP_106717290.1
          Length = 380

 Score =  210 bits (534), Expect = 6e-59
 Identities = 118/359 (32%), Positives = 187/359 (52%), Gaps = 2/359 (0%)

Query: 3   IKEHLKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLALYP 62
           +++ + +L PY  G  +  V   YG  K+ KLASNENP G S         +   L LYP
Sbjct: 8   VRDEVHELAPYNSGLTVREVNERYGPAKIAKLASNENPLGPSPDLDSITMADSDLLRLYP 67

Query: 63  DGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNA 122
           D     LR  ++  L+V+ T +I GNGS+E+I IICRA L  +   VT  P+FP ++  A
Sbjct: 68  DPAGVELREAIAVALDVASTQIILGNGSEELISIICRAVLRPRDRVVTLYPSFPLHEDYA 127

Query: 123 VIEGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVP 182
            + GA V  + ++ + S D+D   + I    ++V   +P NP G++ +  EL   +    
Sbjct: 128 ALMGASVERVNVKGNMSVDVDTFEKKIATPARMVIFSNPMNPVGSWLAPAELSRVIAAAD 187

Query: 183 SRVLVVLDEAYYEYVTAEDYPETVPLL-SKYSNLMILRTFSKAYGLAALRVGYG-IADEN 240
              L+V+DEAY EY   EDY   + LL       ++LRT SKAYGLA LR+GYG +AD  
Sbjct: 188 KNTLIVVDEAYAEYAAGEDYVSAIDLLKGSRRPWVVLRTMSKAYGLAGLRIGYGVVADPE 247

Query: 241 LIRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPS 300
               ++  R PFN + + Q +A+ AL D+  +   V    +  Q+   F   +      S
Sbjct: 248 FRSLLDRVRTPFNVNAIAQVSAVKALADRQHLQRVVTLAASERQRVQAFLLANDWPVAAS 307

Query: 301 QTNFVLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEI 359
           + NF+  D    A +  + LL  G IV+     G+ T +R+++G+ ++N + ++ +  +
Sbjct: 308 KGNFLFFDCAGNAADFAEGLLRYGVIVKPWKQAGYETFVRVSVGSPDENNQFMSAVLSL 366


Lambda     K      H
   0.317    0.134    0.382 

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: 333
Number of extensions: 15
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: 360
Length of database: 380
Length adjustment: 30
Effective length of query: 330
Effective length of database: 350
Effective search space:   115500
Effective search space used:   115500
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: 49 (23.5 bits)

This GapMind analysis is from Jul 26 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