GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Thiomicrorhabdus arctica DSM 13458

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_019555867.1 F612_RS0100950 diaminobutyrate--2-oxoglutarate transaminase

Query= curated2:Q8ZV07
         (383 letters)



>NCBI__GCF_000381085.1:WP_019555867.1
          Length = 428

 Score =  179 bits (454), Expect = 1e-49
 Identities = 128/404 (31%), Positives = 212/404 (52%), Gaps = 34/404 (8%)

Query: 7   YYREYGIRIVKGFMQYVWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIW-AVP 65
           Y R +     K  M  +WD  G+RYID     G +  GH NPKI +AV   ++       
Sbjct: 16  YIRSFPTIFEKSKMAEIWDVSGKRYIDFFAGAGALNYGHNNPKINDAVISYLQNDGIGHA 75

Query: 66  LNFATPARERFIEEF-SKLLPPK---FGVVFLQNTGTEAVEVAIKIAKKVTRKPTIVAFT 121
           L+  T A+  F+E F + +L P+   + + F+  TGT A+E A+KIA+KV  +  I++FT
Sbjct: 76  LDMGTVAKRDFMESFVNNILKPRDLDYKLQFVGPTGTGAIEAALKIARKVKGRKQIMSFT 135

Query: 122 NSFHGRTMGSLSITWNEKY--KKAFEPLYP-HVRFGKFNVPHEVD------KLIGEDT-- 170
           N FHG +MGSLSIT N+ Y  +    P Y   V F K+ +  +VD      K++ +D+  
Sbjct: 136 NGFHGMSMGSLSITGNKYYHDESYGVPGYTTQVPFHKY-LGDKVDTIAYLRKILEDDSSG 194

Query: 171 ----CCVVVEPIQGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQK 226
                 +V+E +Q EGG+N A  E+LK LR+       L+I D++Q G GR+G  ++F++
Sbjct: 195 TELPAAIVLETVQAEGGINVAGEEWLKDLRQICDDFDILMIVDDIQVGNGRSGDFFSFER 254

Query: 227 YGVEPDIFTAGKPVAGGLPIGLAVAREDFGDVFEPGEHGSTFAGNAVVMAAAAAASRLLR 286
            G++PDI T  K +  G P+ L + + +  D++  GEH  TF GN +   A+  A     
Sbjct: 255 AGIKPDIITLSKSIGAGHPMALVLLKPEL-DIWTAGEHSGTFRGNNLAFVASTVALDTYW 313

Query: 287 EEDVPGRAERIGAELA----KALGDTGSRLAVRVKGMGLMLGLELRVKA--DQFIQPLLE 340
            +D   +  +I A+L     + L      +    +G+G++ G E +  +          E
Sbjct: 314 SDDSFSKEVKIKAKLVEQRMQKLVSRFPEIINETRGLGMIWGAEFKDPSITSAICSQAFE 373

Query: 341 RGVMALTAGVNT--LRFLPPYMISKEDV----EVVHAAVTEVLK 378
            G++  TAG  +  ++FL P ++++E +    +++  A+ +VLK
Sbjct: 374 DGLVIETAGAESDLIKFLGPLVMTEELINEGFDILENAIVKVLK 417


Lambda     K      H
   0.320    0.138    0.408 

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: 372
Number of extensions: 21
Number of successful extensions: 4
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: 383
Length of database: 428
Length adjustment: 31
Effective length of query: 352
Effective length of database: 397
Effective search space:   139744
Effective search space used:   139744
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 Apr 10 2024. The underlying query database was built on Apr 09 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