GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Enterococcus termitis LMG 8895

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_069664972.1 BCR25_RS17850 PLP-dependent aminotransferase family protein

Query= SwissProt::H3ZPL1
         (417 letters)



>NCBI__GCF_001730305.1:WP_069664972.1
          Length = 480

 Score =  171 bits (434), Expect = 3e-47
 Identities = 121/407 (29%), Positives = 209/407 (51%), Gaps = 28/407 (6%)

Query: 14  PTLDYEKYFSEKALGMKASEIRELLKLVETS--DVISLAGGLPAPETFPVEIIGEIT-KE 70
           P  D+  Y  + A       + ++ +L+ +S  D++ +  G    +  P      +T K 
Sbjct: 86  PRTDWRHYLEQNAFAKVDPYLEQIEQLIHSSADDLLDVYTGELPLDLIPSFAFPPLTWKH 145

Query: 71  VLEKHAAQALQYGTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFI 130
            LE+     L      G+ PLR +L++ M++ YD  +     + TSG+QQAL LI +V +
Sbjct: 146 FLEEEQQDDL------GYLPLRESLSQDMQKEYDFTLPPESFLITSGAQQALFLILQVLL 199

Query: 131 NPGDIIVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVY 190
            PGD + +E P++L AL  F+        + +D EG+ +D LE+ +++      ++K+V 
Sbjct: 200 QPGDSVAIEDPSFLYALPIFQAAGIRLYGVKMDQEGICIDSLEKTIRQ-----HRIKMVM 254

Query: 191 TIPTFQNPAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRY-SGEPVKPIKAWDEEGR 249
             P+FQNP G TM+ KRRK+L+EL   Y   I+ED+ + +L + S E V+P+K  D E  
Sbjct: 255 VNPSFQNPTGKTMSMKRRKQLIELCQNYQIPILEDDVFAKLNFVSTEQVQPLKKLDPE-N 313

Query: 250 VIYLGTFSKILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDK 309
           V+Y+G+ SKIL    +IGW++A     ++L  A++ +D   + F QV+A         D 
Sbjct: 314 VLYIGSLSKILGSTTKIGWLSAPASVNQQLAEARKMMDFSLSIFPQVLA----NLALTDN 369

Query: 310 HIPKIIEFYKPRRDAMLKALEEFMPDGVKW--TKPEGGMFVWATLPEGIDTKLMLEKAVA 367
           +  K I   +   +A  +A+ + M    +W   +P+GG ++WA    G   +      + 
Sbjct: 370 NFSKKITELRQEVEARGQAVFDLMSKMEEWEVARPKGGYYLWAKWKNGDLRQKDWALFLQ 429

Query: 368 KGVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKI---REGIKRLAETI 411
           +G+   P   F   RD   ++R+NF+ V    I   +E ++R+ E I
Sbjct: 430 EGLLLAPSFFFSESRD---SIRINFSRVSSHNIVEFKEKLERITEKI 473


Lambda     K      H
   0.318    0.137    0.398 

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: 472
Number of extensions: 26
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 417
Length of database: 480
Length adjustment: 33
Effective length of query: 384
Effective length of database: 447
Effective search space:   171648
Effective search space used:   171648
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: 51 (24.3 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