GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Caldicellulosiruptor hydrothermalis 108

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_013403486.1 CALHY_RS08135 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::P58350
         (410 letters)



>NCBI__GCF_000166355.1:WP_013403486.1
          Length = 397

 Score =  298 bits (764), Expect = 1e-85
 Identities = 158/396 (39%), Positives = 239/396 (60%), Gaps = 2/396 (0%)

Query: 15  ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74
           + R  +I  S  L I + A  +K  G+ VI  GAGEPDFDTP+++K AA  AI +G TKY
Sbjct: 4   SQRALNISASPTLAIDSLAKKLKEAGENVIGFGAGEPDFDTPDNIKYAAISAIVKGYTKY 63

Query: 75  TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134
           T + G   LK+AI + ++    + Y  DE+ V+ GAK  L N   A L+ GDEV++P+PY
Sbjct: 64  TPVAGISCLKEAIAKYYKENYEVDYSPDEVVVSNGAKHSLMNVFFALLNDGDEVLLPSPY 123

Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194
           W +Y +++ +  GK V++       +++T   LE   T +T+ ++LNSPSNP+G  Y+  
Sbjct: 124 WVTYPELIKLAGGKVVVVPTTKEKNYKITLSDLEKYTTSKTKAIVLNSPSNPTGMVYTYE 183

Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254
           + + ++E  +    ++++ D++Y+ ++YDG + ++ A +    K   + VNGVSK+YAMT
Sbjct: 184 ELKQIVEFCIER-EIFIVSDEIYDKLIYDGKKHISAASINEKAKEFVIVVNGVSKSYAMT 242

Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314
           GWRIGY    +E  K M+ +QS  TS P+SI+Q A+  AL GPQD +K+    F++RRDL
Sbjct: 243 GWRIGYTLSNKEFTKIMSNLQSHTTSNPNSIAQYAAYEALVGPQDSVKKMICEFEKRRDL 302

Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374
           + + +N    L    PEGAFY +   +  +GK +  GK I +   F   LLE   VAVVP
Sbjct: 303 IYSLVNDTKFLSALKPEGAFYIWVDISAAVGK-SFEGKLIDSANTFAKLLLEVEKVAVVP 361

Query: 375 GSAFGLSPFFRISYATSEAELKEALERIAAACDRLS 410
              FG+    R+SYATSE  ++E LERI    ++LS
Sbjct: 362 SEGFGMENHIRLSYATSEKNIREGLERIKRFVEKLS 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: 391
Number of extensions: 20
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 Sep 24 2021. 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