GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Bacteroides thetaiotaomicron VPI-5482

Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate 351943 BT2415 aspartate aminotransferase (NCBI ptt file)

Query= SwissProt::P58350
         (410 letters)



>FitnessBrowser__Btheta:351943
          Length = 397

 Score =  342 bits (876), Expect = 2e-98
 Identities = 178/397 (44%), Positives = 259/397 (65%), Gaps = 3/397 (0%)

Query: 13  QPASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGET 72
           Q + R++S+  S  L +  ++  +K +G  VI L  GEPDF+TP+H+K+AA  AI    +
Sbjct: 3   QLSDRLNSLSPSATLAMSQKSNELKAQGIDVINLSVGEPDFNTPDHIKEAAKKAIDDNFS 62

Query: 73  KYTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPT 132
           +Y+ + G P L+ AI EK ++ENGL Y   +I+ A GAKQ + NA++  ++PGDEVI+P 
Sbjct: 63  RYSPVPGYPALRNAIVEKLKKENGLEYTAAQISCANGAKQSVCNAILVLVNPGDEVIVPA 122

Query: 133 PYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYS 192
           PYW SY ++V + EG PV+++      F++T ++LEAAITP+T+ ++L SPSNP+G+ YS
Sbjct: 123 PYWVSYPEMVKMAEGTPVIVSAGIEQDFKITPKQLEAAITPKTKALILCSPSNPTGSVYS 182

Query: 193 AADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYA 252
             +   L  VL ++P V ++ D++YEHI Y G    + AQ  P +K RT+ VNGVSKAYA
Sbjct: 183 KEELAGLAAVLAKYPQVVVIADEIYEHINYIG-AHQSIAQF-PEMKERTVIVNGVSKAYA 240

Query: 253 MTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRR 312
           MTGWRIG+  GP  ++KA   +Q Q TS P S+SQ A+ AA  G Q+ +KE  ++F+RRR
Sbjct: 241 MTGWRIGFIAGPEWIVKACNKLQGQYTSGPCSVSQKAAEAAYVGTQEPVKEMQKAFERRR 300

Query: 313 DLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAV 372
           DL+V     + G +  VP+GAFY F  C+   GK +   ++I+   D   YLLEDAHVA 
Sbjct: 301 DLIVKLAKEVPGFEVNVPQGAFYLFPKCSYFFGK-SNGERKIENSDDLAMYLLEDAHVAC 359

Query: 373 VPGSAFGLSPFFRISYATSEAELKEALERIAAACDRL 409
           V G++FG     R+SYATS+  + EA+ RI  A  +L
Sbjct: 360 VGGTSFGAPECIRMSYATSDENIVEAIRRIKEALAKL 396


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: 448
Number of extensions: 19
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 17 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