GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Desulfovibrio vulgaris Hildenborough

Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate 208745 DVU3223 aspartate aminotransferase

Query= SwissProt::P58350
         (410 letters)



>MicrobesOnline__882:208745
          Length = 390

 Score =  286 bits (731), Expect = 1e-81
 Identities = 155/389 (39%), Positives = 230/389 (59%), Gaps = 7/389 (1%)

Query: 15  ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74
           + R++ I  S  L + A+A  +K  G  V+ L  GEPDF TP H+ +AA  AI  G T+Y
Sbjct: 4   SDRLTRIKPSATLAVNAKALELKARGVKVVSLAVGEPDFGTPAHICEAAKRAIDEGFTRY 63

Query: 75  TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134
           T + G  EL++A+   F R  G+    +   V  G KQ L+N   A L+PGDEV++P PY
Sbjct: 64  TPVPGIIELREAVAGYFGRCYGVEAPAEATIVTNGGKQALYNLFQALLNPGDEVLVPAPY 123

Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194
           W SY  +V + EG PV +   A  GF++T  +L+A  TPRTR +LLNSPSNP+GA Y+  
Sbjct: 124 WVSYPALVQLAEGVPVFVPSPAERGFKITPAELDAHRTPRTRVLLLNSPSNPTGACYTRE 183

Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254
           +   L++  + H  ++++ D++Y+ +VY   + V+ +       +R   VNG++K +AMT
Sbjct: 184 EMDALMQWAVDH-DIFVIADEIYDRLVYGDMQPVSVSGWWQRFPDRVAVVNGLAKTFAMT 242

Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314
           GWR+GY     +L+KA+A +Q Q+TS   SI+Q A++AAL GP D ++E   +F RRRDL
Sbjct: 243 GWRVGYVLAHPDLVKAVAKIQGQSTSNICSIAQKAALAALTGPYDAVEEMRCAFVRRRDL 302

Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374
             + ++    + C  P+GAFY F+          P    +      C  LLE+A VA+VP
Sbjct: 303 AYDIISGWKDVVCPRPDGAFYLFADIHRHYNASMPDSAAV------CTRLLEEAQVALVP 356

Query: 375 GSAFGLSPFFRISYATSEAELKEALERIA 403
           GSAFG     R SYA ++  L++AL R+A
Sbjct: 357 GSAFGDDKCIRFSYAVADDVLEDALSRVA 385


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: 438
Number of extensions: 18
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: 390
Length adjustment: 31
Effective length of query: 379
Effective length of database: 359
Effective search space:   136061
Effective search space used:   136061
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