GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Flavobacterium glycines Gm-149

Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_066326077.1 BLR17_RS14015 histidinol-phosphate transaminase

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



>NCBI__GCF_900100165.1:WP_066326077.1
          Length = 349

 Score =  173 bits (439), Expect = 5e-48
 Identities = 116/365 (31%), Positives = 190/365 (52%), Gaps = 34/365 (9%)

Query: 3   IKEHLKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLALYP 62
           I+E++K LKPY   +       ++   ++V L +NENPY                +  YP
Sbjct: 10  IRENVKVLKPYSSARD---EFEDFDTAEMVFLDANENPYQ-------------NGVNRYP 53

Query: 63  DGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKT-NTVTAAPTFPQYKHN 121
           D   A ++  L    N++   ++ GNGSDE++ ++ RAF   K  N +T  PT+  Y   
Sbjct: 54  DPQQANVKVALGAIKNLNPQQILLGNGSDEVLDLLFRAFCEPKVDNVITLPPTYGMYGVL 113

Query: 122 AVIEGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERV 181
           A I   E +EI L  D    +D +LEA+   T+++++CSPNNPTG   +   +   LE+ 
Sbjct: 114 ANINNVENKEILLTNDFQPQVDKILEAVTPTTKLIFLCSPNNPTGNSFTTESVTTLLEKF 173

Query: 182 PSRVLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENL 241
                VV+DEAY ++    D    +  L +Y NL+I +T SKAYGLA +R+G   A   +
Sbjct: 174 NG--FVVIDEAYIDF---SDKASWLEKLDQYPNLIITQTLSKAYGLAGIRLGICYASTEV 228

Query: 242 IRQIEPAREPFNTSRLGQAAAIAALDDQ----AFIASCVEQNNAGLQ--QYYDFAKTHGL 295
           I  +   + P+N + L Q  A+  L+DQ      I+S +E+ +  L    +  F +    
Sbjct: 229 IAVLNKIKPPYNVNELTQQRALERLNDQEKINREISSILEERDTLLDVLNHVSFVE---- 284

Query: 296 KCYPSQTNFVLIDFKRPADELFQALLEKGYIVRSGNALGF-PTSLRITIGTKEQNEEILA 354
           K YP++ NF+LI     A++ +  L+ KG ++R+         +LR+TIGT E+N++++ 
Sbjct: 285 KIYPTEANFILIKVD-DANKRYDELIAKGIVIRNRTTQPLCENTLRLTIGTAEENKKLMK 343

Query: 355 ILAEI 359
            L E+
Sbjct: 344 ALTEL 348


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: 332
Number of extensions: 23
Number of successful extensions: 5
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: 349
Length adjustment: 29
Effective length of query: 331
Effective length of database: 320
Effective search space:   105920
Effective search space used:   105920
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