GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Hydrogenovibrio halophilus DSM 15072

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_019895362.1 A377_RS0106195 diaminobutyrate--2-oxoglutarate transaminase

Query= curated2:Q8ZV07
         (383 letters)



>NCBI__GCF_000384235.1:WP_019895362.1
          Length = 417

 Score =  184 bits (467), Expect = 4e-51
 Identities = 132/408 (32%), Positives = 207/408 (50%), Gaps = 35/408 (8%)

Query: 4   IAKYYREYGIRIVKGFMQYVWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWA 63
           I  Y R Y    VKG     WD+ G+ YID     GV+  GH NPK+  A+   + E   
Sbjct: 11  IRAYSRAYPAVFVKGQNAKQWDETGKEYIDFYAGAGVLNFGHNNPKLKAAMMDYLAEDGV 70

Query: 64  V-PLNFATPARERFIEEFSK-LLPPK---FGVVFLQNTGTEAVEVAIKIAKKVTRKPTIV 118
           +  L+  T A+  FI+ F + +L P+   + + F+  TGT AVE A+K+A+KVT +  ++
Sbjct: 71  LHSLDMMTAAKRDFIQGFVETILQPRKMDYKLQFMGPTGTNAVEAALKLARKVTGRQNVI 130

Query: 119 AFTNSFHGRTMGSLSITWNEKYKKAFEPLYPHVRFGKF--NVPHEVDKLI---------- 166
           AF   FHG T+G+L+ T N  +++A      HV    F  NV   +  L           
Sbjct: 131 AFAQGFHGMTLGALACTANGYFRQAAGVPLNHVSHCPFETNVGGGLAMLDTLRALYDNTS 190

Query: 167 --GEDTCCVVVEPIQGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAF 224
              E    ++VEPIQ EGGVN A+ E+L+ L + A+  GALLI D++Q G GRTG  ++F
Sbjct: 191 GGAEKPAAILVEPIQAEGGVNVASAEWLQGLDKLAKDLGALLIVDDIQAGCGRTGQYFSF 250

Query: 225 QKYGVEPDIFTAGKPVAG-GLPIGLAVAREDFGDVFEPGEHGSTFAGNAVVMAAAAAASR 283
            + G++PDI T  K + G G PI + + + +    ++PGEH  TF G  +   A   A R
Sbjct: 251 DEAGIDPDIITLAKGLGGLGTPIAMNLVKPEHDQHWQPGEHTGTFRGQNLSFVAGREALR 310

Query: 284 LLREEDVPGRAE-----RIGA--ELAKALGDTGSRLAVRVKGMGLMLGLELRVKADQFIQ 336
              ++ +           +GA  ++A+   D G   +VR KGM   L +     A    +
Sbjct: 311 YFEDDQLMNAVHDKGEIMVGALEQMAQTYPDAG--FSVRGKGMMQALDVGDGALAKAVAR 368

Query: 337 PLLERGVMALTAGV--NTLRFLPPYMISKED----VEVVHAAVTEVLK 378
              ERG++    GV  + ++ +PP  I +++    +E++  A+   +K
Sbjct: 369 ECFERGMLFGPCGVGGSVIKLIPPLTIPEDELVAGLEILSEALAACMK 416


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: 378
Number of extensions: 24
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: 417
Length adjustment: 31
Effective length of query: 352
Effective length of database: 386
Effective search space:   135872
Effective search space used:   135872
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