GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Streptacidiphilus oryzae TH49

Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_037580662.1 BS73_RS22465 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= CharProtDB::CH_004890
         (393 letters)



>NCBI__GCF_000744815.1:WP_037580662.1
          Length = 419

 Score =  149 bits (375), Expect = 2e-40
 Identities = 121/392 (30%), Positives = 186/392 (47%), Gaps = 29/392 (7%)

Query: 13  STTLAITAKAKELKAAGHDVIGLGAGEPDFNTPQHIIDAAVRSMNEGHTKYTPSGGLAEL 72
           S TLAI    +  +AAG  V+ LG GE     P  +  AAV +       Y P  G AE 
Sbjct: 5   SATLAIDETLRARRAAGEKVLHLGFGEAGLPVPAGV--AAVLADAVRRNGYGPVAGSAEA 62

Query: 73  KNSIAEKFKRDQNIEYKPSQIIVCTGAKHALYTLFQVILDEEDEVIIPTPYWVSYPEQVK 132
           + + A  F R + +   P Q++   G+K  L+ L   +L    +V++P P WVSY  Q  
Sbjct: 63  REAAAGWFTR-RGLPTGPEQVLFAPGSKALLFAL---VLALPGDVVLPRPSWVSYAAQSA 118

Query: 133 LAGGKPVYVEGLEENHFKISPEQLKNAITEKTKA-------IVINSPSNPTGVMYTEEEL 185
           LAG + + V           PE+L+ A+ E+ +A       +V+  P NPTG +   E++
Sbjct: 119 LAGKRTIGVPIPAGAGGVPDPERLEGAL-ERARAEGAEPGVLVLTVPDNPTGTVARAEDV 177

Query: 186 SALGEVCLEHDILIVSDEIYEKLTYGGKKHVSIAQLSDRLKEQTVIINGVSKSHSMTGWR 245
            A+  +   H + +V+DEIY +L +      ++ +  D L E+TV+ +G+SKS ++ GWR
Sbjct: 178 RAVCGIAERHGLAVVADEIYAELVHDADAARALPRAVDHLPERTVVTSGLSKSMALGGWR 237

Query: 246 IGYA-----AGSEDIIKAMTNLASHSTSNPTSIAQYGAIAAYNGPSEPLEEMREAFEHRL 300
           IG+A     A  E +   +  +AS   S+  +  Q  A      P E L  +  A   RL
Sbjct: 238 IGFARLPEGAWGERLRGELVGVASEIWSSLAAPMQAVAARVLEDPPEVLAHIAAA--RRL 295

Query: 301 NTIYAKLIE----IPGFSCVKPEGAFYLFPN---AKEAAQSCGFKDVDEFVKALLEEEKV 353
           +   A+ +       G  C  PE  FYL+P+    +E   + G +   E   ALLE   V
Sbjct: 296 HGAVARAVHAEFAAAGAVCRAPEAGFYLYPDFEPVRERLAARGVRSGAELAAALLERYGV 355

Query: 354 AIVPGSGFG-SPENVRLSYATSLDLLEEAIER 384
            ++ G+ FG +   +R   ATSL   E   ER
Sbjct: 356 GVLAGAAFGDAAAGLRARVATSLLYGETEAER 387


Lambda     K      H
   0.313    0.131    0.370 

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: 376
Number of extensions: 17
Number of successful extensions: 5
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: 393
Length of database: 419
Length adjustment: 31
Effective length of query: 362
Effective length of database: 388
Effective search space:   140456
Effective search space used:   140456
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 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