GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Thiohalospira halophila DSM 15071 HL 3

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_093427355.1 BM272_RS03610 histidinol-phosphate transaminase

Query= reanno::BFirm:BPHYT_RS14905
         (370 letters)



>NCBI__GCF_900112605.1:WP_093427355.1
          Length = 373

 Score =  343 bits (881), Expect = 3e-99
 Identities = 181/362 (50%), Positives = 240/362 (66%), Gaps = 8/362 (2%)

Query: 10  VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69
           VR +APY  GKP++E+ RE+G+ +A  +KLASNENPLG    A+ A A    E G YPD 
Sbjct: 12  VRGLAPYKPGKPVAELQREYGVADA--IKLASNENPLGASPRAREAAAATLDEAGIYPDG 69

Query: 70  NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129
             F L+  +++ +GV A+ VTLGNGS+D L  A   FV  G  +VY+ ++FA+Y L TQ 
Sbjct: 70  GGFALRGRIADHHGVAAEQVTLGNGSSDPLAFAVEVFVTPGDEVVYSAHAFALYPLLTQA 129

Query: 130 LGARAIVVPAVK-YGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRH 188
            GAR + VP    YGHDL+AM AA++D TR++FVANPNNPTGT +    L  FL++VP H
Sbjct: 130 AGARGVEVPTTAGYGHDLEAMAAAITDRTRVVFVANPNNPTGTRVGASALRNFLERVPGH 189

Query: 189 VVVVLDEAYTEYLPQ-EKRY-DSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELT 246
            + V+DEAY EY    +  Y D+ AW+  +PNLLV+RTFSK  GLAGLRVG+ ++ P + 
Sbjct: 190 TLAVVDEAYFEYARDLDSDYPDASAWLAEFPNLLVTRTFSKLHGLAGLRVGYGLSSPAVA 249

Query: 247 DLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDG 306
           DLLNRVR PFNVN  AQAAA+AA++D   L  S   N +G  +L     + GL+++PS G
Sbjct: 250 DLLNRVRPPFNVNAPAQAAALAAMDDAEHLAASLEANREGMAQLEAGLRERGLDWIPSVG 309

Query: 307 NFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERT 366
           NF+    G D      V+  LL+QGVI+RP+G YGLP+ LR TIG   +NE  + AL+R 
Sbjct: 310 NFLTFDTGGD---AGEVHEALLRQGVILRPMGEYGLPRHLRATIGRTADNERLLTALDRA 366

Query: 367 LA 368
           LA
Sbjct: 367 LA 368


Lambda     K      H
   0.318    0.135    0.385 

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: 413
Number of extensions: 25
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: 370
Length of database: 373
Length adjustment: 30
Effective length of query: 340
Effective length of database: 343
Effective search space:   116620
Effective search space used:   116620
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: 49 (23.5 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