GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Lentibacillus jeotgali Grbi

Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_010530816.1 ON01_RS09560 histidinol-phosphate transaminase

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



>NCBI__GCF_000224785.1:WP_010530816.1
          Length = 368

 Score =  365 bits (937), Expect = e-105
 Identities = 185/359 (51%), Positives = 244/359 (67%), Gaps = 1/359 (0%)

Query: 1   MRIKEHLKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLAL 60
           M+ K+ LK++ PYQPGK  E VK EYGL+++VKLASNENP+G S    + L  +   L +
Sbjct: 1   MKSKQILKEMTPYQPGKQTEEVKKEYGLNRIVKLASNENPFGYSRKVDDYLSGQKPALNI 60

Query: 61  YPDGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKH 120
           YPDGY++ LRT L   L VSE  LIFGNG+DE++QII RA+L    NTV AAPTFPQYKH
Sbjct: 61  YPDGYTSKLRTALVNKLEVSEHQLIFGNGTDEVVQIIGRAYLYPGVNTVMAAPTFPQYKH 120

Query: 121 NAVIEGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLER 180
           NA+IEGAEV+E+    +G HDL  MLE ID+ T VVW+CSPNNPTG      +L  FL +
Sbjct: 121 NALIEGAEVKEVPTI-NGYHDLQGMLEVIDDNTNVVWLCSPNNPTGALIPRDDLYEFLGK 179

Query: 181 VPSRVLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADEN 240
            PS +LVVLDEAY+EY  ++  P+ +  L +Y NL++LRTFSKAYGLA LR+GYGIA+E 
Sbjct: 180 CPSDILVVLDEAYFEYADSQKQPDVLQHLHQYKNLVVLRTFSKAYGLAGLRIGYGIANEE 239

Query: 241 LIRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPS 300
           LI +++  R PFNTS + Q AAIAALDD  F+   + +NN   Q +  F  + G   Y S
Sbjct: 240 LIPRLDVVRGPFNTSSIAQQAAIAALDDDEFLKDSISRNNKIKQSFEQFLNSIGWPFYDS 299

Query: 301 QTNFVLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEI 359
           QTNF+L+       + F  L E G+IVR    LG   ++R+TIGT++  +E+  +L ++
Sbjct: 300 QTNFLLVSTPISGKKAFHFLQENGFIVRPVEGLGSSETIRVTIGTEKDMQELQDVLYQL 358


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: 387
Number of extensions: 13
Number of successful extensions: 2
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: 368
Length adjustment: 29
Effective length of query: 331
Effective length of database: 339
Effective search space:   112209
Effective search space used:   112209
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