GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Desulfoscipio geothermicus DSM 3669

Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate WP_092483105.1 BM299_RS08755 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::P58350
         (410 letters)



>NCBI__GCF_900115975.1:WP_092483105.1
          Length = 397

 Score =  345 bits (885), Expect = 1e-99
 Identities = 184/396 (46%), Positives = 253/396 (63%), Gaps = 2/396 (0%)

Query: 15  ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74
           A R  +I  S  L I A+A  M  EG  VI  GAGEPDF TPE++KQA   AI    T+Y
Sbjct: 4   AERAKNISPSPTLSIDAQAKKMIAEGIKVINFGAGEPDFGTPENIKQAGVKAIENDMTRY 63

Query: 75  TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134
           T + G   L++AI +K   +NGL YE  +I V+ GAK  L+NA       GDEVI+P PY
Sbjct: 64  TPVAGIEPLRRAIVKKLAEDNGLDYEPGQIVVSAGAKHSLYNAFQVLCQEGDEVILPAPY 123

Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194
           W SY + + +   +PV+++    + F+LT ++L  AITP TR ++LNSPSNP+GA Y+  
Sbjct: 124 WVSYLEQIKLTGARPVIVSTRVENNFKLTPDELRRAITPNTRLIVLNSPSNPTGAVYTGD 183

Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254
           +   L E+L ++  + ++ D++YE ++YDG   V+ A L PGLK  T+ +NGVSK+YAMT
Sbjct: 184 ELVALGEILEQN-KIAVISDEIYEKLIYDGLEHVSIAALSPGLKELTVVINGVSKSYAMT 242

Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314
           GWRIGYA  P  + KAMA +QS +TS P+SI+QAASV AL G Q+ +++    F +RRD 
Sbjct: 243 GWRIGYAAAPAPVAKAMADLQSHSTSNPTSIAQAASVEALEGTQEPVRQMVAEFVKRRDY 302

Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374
           +V  LNA+ G++C  P GAFY F     +LGK +  G +I + +D    LLE AHVA+VP
Sbjct: 303 MVERLNAMPGVNCNRPGGAFYVFPEIKPLLGK-SYEGVKIDSASDLAKVLLEKAHVAIVP 361

Query: 375 GSAFGLSPFFRISYATSEAELKEALERIAAACDRLS 410
           G AFG    FR+SYATS   ++E L+RI     +LS
Sbjct: 362 GIAFGDDTCFRLSYATSMDNIREGLDRIEKVLQQLS 397


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: 450
Number of extensions: 26
Number of successful extensions: 3
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: 397
Length adjustment: 31
Effective length of query: 379
Effective length of database: 366
Effective search space:   138714
Effective search space used:   138714
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 Apr 09 2024. The underlying query database was built on Sep 17 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:

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