GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Halomonas desiderata SP1

Align tyrosine aminotransferase (EC 2.6.1.57) (characterized)
to candidate WP_086508794.1 BZY95_RS04550 amino acid aminotransferase

Query= reanno::pseudo6_N2E2:Pf6N2E2_2632
         (397 letters)



>NCBI__GCF_002151265.1:WP_086508794.1
          Length = 395

 Score =  488 bits (1257), Expect = e-142
 Identities = 232/391 (59%), Positives = 306/391 (78%)

Query: 3   FDAIGRVPGDPILGLMEAYGADANPSKFDLGVGVYKDAQGLTPILQSVKQAEQRLVDRQT 62
           F+ I RVPGD ILGL+EA+  D NP K DLGVGVYKDAQG TP++++VK+AE  L+  +T
Sbjct: 2   FEHIERVPGDAILGLIEAFKKDTNPQKVDLGVGVYKDAQGNTPVMRAVKEAEALLLKNET 61

Query: 63  TKTYIGGHGDAAFGQLINELVLGADSPLISAKRAGATQTPGGTGALRLSADFIAQCLPGR 122
           TKTYIG HG   +G+++  +VLG DSP+++AKRA ATQ+PGGTGALRL+ADFI+  LPG+
Sbjct: 62  TKTYIGSHGAPQYGEVVLPMVLGQDSPVLAAKRASATQSPGGTGALRLAADFISTQLPGK 121

Query: 123 GVWLSNPTWPIHETIFAAAGVKVGHYPYVGADNRLDFEAMLATLNQAPKGDVVLLHACCH 182
            +W+S+PTWP H  IF AAG+++  YPYV A+NRLDF  MLA + Q P GDV++LHACCH
Sbjct: 122 SIWVSDPTWPNHHGIFKAAGIELHKYPYVDAENRLDFAGMLAAVKQIPAGDVIVLHACCH 181

Query: 183 NPTGFDLSHEQWRQVLEVVRDRDLLPLIDFAYQGFGDGLEQDAWAVRLFAQALPEVLVTS 242
           NPTGFDL   QW+Q+LEVVR+R+LLPLIDFAYQGFG+GL++DA+ VRL A+ L EV++TS
Sbjct: 182 NPTGFDLDRGQWQQILEVVRERNLLPLIDFAYQGFGEGLDEDAYGVRLMAENLDEVIITS 241

Query: 243 SCSKNFGLYRDRTGALIVCARDAEKLVDIRSQLANIARNLWSTPPDHGAAVVATILGNPE 302
           SCSKNFG+Y +RTG LI+ A+++E++ ++RSQ+A +AR  +S PP HG A+V+ IL + E
Sbjct: 242 SCSKNFGIYCERTGCLIMVAKNSEQMENVRSQVAIVARENYSNPPAHGGAIVSEILHSAE 301

Query: 303 LKSLWADEVQAMRLRIAQLRSGLLEALEPHGLRERFAHIGVQRGMFSYTGLTPEQVKHLR 362
           L +LW +E+  MR RI  LR   +E+L+P+GL +++A +  QRGMFSYTGL PEQV  LR
Sbjct: 302 LAALWREELTEMRDRINTLRRDFVESLKPYGLDQKYACVAEQRGMFSYTGLKPEQVDRLR 361

Query: 363 ERHSVYMVGTGRANVAGIDATRLDLLAEAIA 393
           +   +YMV +GRANVAG     L  LA+AIA
Sbjct: 362 DEFGIYMVRSGRANVAGFSHENLPYLAKAIA 392


Lambda     K      H
   0.321    0.137    0.419 

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: 514
Number of extensions: 14
Number of successful extensions: 1
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: 397
Length of database: 395
Length adjustment: 31
Effective length of query: 366
Effective length of database: 364
Effective search space:   133224
Effective search space used:   133224
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 (21.8 bits)
S2: 50 (23.9 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