GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO8 in Desulfoscipio geothermicus DSM 3669

Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_092483105.1 BM299_RS08755 pyridoxal phosphate-dependent aminotransferase

Query= CharProtDB::CH_017144
         (393 letters)



>NCBI__GCF_900115975.1:WP_092483105.1
          Length = 397

 Score =  416 bits (1069), Expect = e-121
 Identities = 206/394 (52%), Positives = 275/394 (69%), Gaps = 4/394 (1%)

Query: 1   MKLAKRVASLTPSATLAITEKAKELKAAGHDVIGLGAGEPDFNTPQHILDAAIKAMNEGH 60
           MKLA+R  +++PS TL+I  +AK++ A G  VI  GAGEPDF TP++I  A +KA+    
Sbjct: 1   MKLAERAKNISPSPTLSIDAQAKKMIAEGIKVINFGAGEPDFGTPENIKQAGVKAIENDM 60

Query: 61  TKYTPSGGLPALKEEIIKKFARDQGLDYEPAEVIVCVGAKHALYTLFQVLLDEGDEVIIP 120
           T+YTP  G+  L+  I+KK A D GLDYEP +++V  GAKH+LY  FQVL  EGDEVI+P
Sbjct: 61  TRYTPVAGIEPLRRAIVKKLAEDNGLDYEPGQIVVSAGAKHSLYNAFQVLCQEGDEVILP 120

Query: 121 TPYWVSYPEQVKLAGGVPVYVEGLEQNHFKITPEQLKQAITPRTKAVIINSPSNPTGMIY 180
            PYWVSY EQ+KL G  PV V    +N+FK+TP++L++AITP T+ +++NSPSNPTG +Y
Sbjct: 121 APYWVSYLEQIKLTGARPVIVSTRVENNFKLTPDELRRAITPNTRLIVLNSPSNPTGAVY 180

Query: 181 TAEELKALGEVCLAHGVLIVSDEIYEKLTYGGAKHVSIAELSPELKAQTVIINGVSKSHS 240
           T +EL ALGE+   + + ++SDEIYEKL Y G +HVSIA LSP LK  TV+INGVSKS++
Sbjct: 181 TGDELVALGEILEQNKIAVISDEIYEKLIYDGLEHVSIAALSPGLKELTVVINGVSKSYA 240

Query: 241 MTGWRIGYAAGPKDIIKAMTDLASHSTSNPTSIAQYAAIAAYSGPQEPVEQMRQAFEQRL 300
           MTGWRIGYAA P  + KAM DL SHSTSNPTSIAQ A++ A  G QEPV QM   F +R 
Sbjct: 241 MTGWRIGYAAAPAPVAKAMADLQSHSTSNPTSIAQAASVEALEGTQEPVRQMVAEFVKRR 300

Query: 301 NIIYDKLVQIPGFTCVKPQGAFYLFPNARE--AAAMAGCR--TVDEFVAALLEEAKVALV 356
           + + ++L  +PG  C +P GAFY+FP  +     +  G +  +  +    LLE+A VA+V
Sbjct: 301 DYMVERLNAMPGVNCNRPGGAFYVFPEIKPLLGKSYEGVKIDSASDLAKVLLEKAHVAIV 360

Query: 357 PGSGFGAPDNVRLSYATSLDALETAVERIHRFME 390
           PG  FG     RLSYATS+D +   ++RI + ++
Sbjct: 361 PGIAFGDDTCFRLSYATSMDNIREGLDRIEKVLQ 394


Lambda     K      H
   0.316    0.133    0.381 

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: 458
Number of extensions: 21
Number of successful extensions: 2
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: 397
Length adjustment: 31
Effective length of query: 362
Effective length of database: 366
Effective search space:   132492
Effective search space used:   132492
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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