GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysN in Marinobacter adhaerens HP15

Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate GFF1405 HP15_1371 aspartate aminotransferase

Query= SwissProt::P58350
         (410 letters)



>lcl|FitnessBrowser__Marino:GFF1405 HP15_1371 aspartate
           aminotransferase
          Length = 394

 Score =  386 bits (992), Expect = e-112
 Identities = 197/393 (50%), Positives = 270/393 (68%), Gaps = 4/393 (1%)

Query: 13  QPASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGET 72
           Q +SR+ +I  S  L +  +AA ++  G+ +I LGAGEPDFDTP+H+KQAA +AI+ G+T
Sbjct: 4   QLSSRVQAIKPSPTLAVTNKAAELRAAGQDIIGLGAGEPDFDTPDHIKQAAIEAINNGQT 63

Query: 73  KYTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPT 132
           KYTA+DGTP LKKAI  KF+R+NGL YE ++I V++G KQ  FN  +A+L+PGDE IIP 
Sbjct: 64  KYTAVDGTPALKKAIIAKFKRDNGLDYEANQILVSSGGKQSFFNLALATLNPGDEAIIPA 123

Query: 133 PYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYS 192
           PYW SY D+V + EGKPV+I   A + F++T E+LE AIT RTR  ++NSPSNPSG AY+
Sbjct: 124 PYWVSYPDMVLVAEGKPVIIETGAETRFKITPEQLENAITERTRLFVINSPSNPSGMAYT 183

Query: 193 AADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYA 252
             + + + EVL +HP++ +  DDMYE I++ G  F       P L +RT  +NGVSKAY+
Sbjct: 184 LEELQAIGEVLKKHPNIMIATDDMYEPILWTGKPFCNILNATPELYDRTFVLNGVSKAYS 243

Query: 253 MTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRR 312
           MTGWRIGYA GP ++I AM  +QSQ+TS P+SISQAA+ AAL+G Q  + E  ++F+ R 
Sbjct: 244 MTGWRIGYAAGPAKIIGAMKKIQSQSTSNPASISQAAAQAALDGDQGCVGEMVKAFKERH 303

Query: 313 DLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAV 372
           D +V  LN + G++C   +G FY F    G +     +   + TD +F   LL DA VA+
Sbjct: 304 DWLVEALNKLPGVECLNGDGTFYVFPSFQGAI----DADSSVSTDVEFAEKLLTDAGVAL 359

Query: 373 VPGSAFGLSPFFRISYATSEAELKEALERIAAA 405
           VPGSAFG     R+S+ATS   L++A+ER+  A
Sbjct: 360 VPGSAFGCPGHMRLSFATSMENLEKAVERLQKA 392


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: 494
Number of extensions: 22
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: 410
Length of database: 394
Length adjustment: 31
Effective length of query: 379
Effective length of database: 363
Effective search space:   137577
Effective search space used:   137577
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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