GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysN in Cupriavidus basilensis 4G11

Align 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39) (characterized)
to candidate RR42_RS35305 RR42_RS35305 aspartate aminotransferase

Query= reanno::Smeli:SMc04386
         (410 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS35305 RR42_RS35305 aspartate
           aminotransferase
          Length = 401

 Score =  424 bits (1089), Expect = e-123
 Identities = 206/393 (52%), Positives = 274/393 (69%)

Query: 17  RISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTA 76
           R++ I  S     G R   ++  G+ VI L AGEPDF+TP H+++AA  A+  G+T+YT 
Sbjct: 7   RLNRIKPSPSSMAGQRVRELRAAGRDVIGLTAGEPDFETPAHIREAAWRAMQAGKTRYTD 66

Query: 77  LDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWT 136
           + GT EL+ A  +KF+RENGL Y   EI V+TGAKQ++FNA+M ++  GDEVI+P PYW 
Sbjct: 67  VGGTAELRHAAAQKFKRENGLDYAASEIIVSTGAKQVIFNALMCTVQQGDEVIVPAPYWV 126

Query: 137 SYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADY 196
           SY DI     G PV +AC A +GF+LT E+LE AI+ RTRW++LNSP+NPSGAAY+  + 
Sbjct: 127 SYPDITLFAGGVPVFVACQAENGFKLTPEELERAISARTRWLILNSPNNPSGAAYTRTEL 186

Query: 197 RPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGW 256
             + EVL RHPHVW++ DD+YEH+ YDG  FVT AQ  P LK RTLT+NGVSKAYAMTGW
Sbjct: 187 VAIAEVLERHPHVWVMTDDIYEHLTYDGAAFVTLAQAAPSLKARTLTINGVSKAYAMTGW 246

Query: 257 RIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVV 316
           RIGYAG P  LIKAM  +QSQ+TS  ++++QAA++AAL+GPQDF+      FQ RRD VV
Sbjct: 247 RIGYAGAPAPLIKAMVKLQSQSTSGANAVAQAAAIAALDGPQDFIAANKAVFQARRDRVV 306

Query: 317 NGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGS 376
             L  +DG+ C+ P GAFY F+ C  ++G  TP G  I++  D+  ++L+   +AV+ GS
Sbjct: 307 AALGQVDGIHCQAPAGAFYVFASCEALIGARTPHGSVIRSSDDWVNWVLDSQDLAVLQGS 366

Query: 377 AFGLSPFFRISYATSEAELKEALERIAAACDRL 409
           A+G+   FR+S+A S A+L E   RI AA   L
Sbjct: 367 AYGVDTHFRLSFAASMAQLDEGCRRIEAAAAAL 399


Lambda     K      H
   0.318    0.134    0.393 

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: 501
Number of extensions: 17
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: 410
Length of database: 401
Length adjustment: 31
Effective length of query: 379
Effective length of database: 370
Effective search space:   140230
Effective search space used:   140230
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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