GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ARO8 in Marinobacter adhaerens HP15

Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate GFF1405 HP15_1371 aspartate aminotransferase

Query= SwissProt::Q82WA8
         (397 letters)



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

 Score =  515 bits (1327), Expect = e-151
 Identities = 261/396 (65%), Positives = 317/396 (80%), Gaps = 5/396 (1%)

Query: 1   MKLSQRVQAIKPSPTLAVTAKAARLKAEGKNIIGLGAGEPDFDTPLHIKDAAITAIRNGF 60
           ++LS RVQAIKPSPTLAVT KAA L+A G++IIGLGAGEPDFDTP HIK AAI AI NG 
Sbjct: 3   LQLSSRVQAIKPSPTLAVTNKAAELRAAGQDIIGLGAGEPDFDTPDHIKQAAIEAINNGQ 62

Query: 61  TKYTAVGGTASLKQAIISKFKRENSLEFMPGEILVSSGGKQSFFNLVLATIDPGDEVIIP 120
           TKYTAV GT +LK+AII+KFKR+N L++   +ILVSSGGKQSFFNL LAT++PGDE IIP
Sbjct: 63  TKYTAVDGTPALKKAIIAKFKRDNGLDYEANQILVSSGGKQSFFNLALATLNPGDEAIIP 122

Query: 121 APYWVSYPDIVLIAEGKPVFIDTGIEEKFKISPDQLEKAITPRTRMFVVNSPSNPSGSVY 180
           APYWVSYPD+VL+AEGKPV I+TG E +FKI+P+QLE AIT RTR+FV+NSPSNPSG  Y
Sbjct: 123 APYWVSYPDMVLVAEGKPVIIETGAETRFKITPEQLENAITERTRLFVINSPSNPSGMAY 182

Query: 181 SLEELQALGAVLRKYPDILIATDDMYEHILLSGDGFVNILNACPDLKARTVVLNGVSKAY 240
           +LEELQA+G VL+K+P+I+IATDDMYE IL +G  F NILNA P+L  RT VLNGVSKAY
Sbjct: 183 TLEELQAIGEVLKKHPNIMIATDDMYEPILWTGKPFCNILNATPELYDRTFVLNGVSKAY 242

Query: 241 AMTGWRIGYCGGPAAIITAMENIQSQSTSNPNSIAQVAAEAALNGDQSCMVPMIEAFRER 300
           +MTGWRIGY  GPA II AM+ IQSQSTSNP SI+Q AA+AAL+GDQ C+  M++AF+ER
Sbjct: 243 SMTGWRIGYAAGPAKIIGAMKKIQSQSTSNPASISQAAAQAALDGDQGCVGEMVKAFKER 302

Query: 301 NQFLTNALNSIAGIHCLLSEGAFYAFVDVRQAISRLNTQQILQNSSDIAFCNYVLEKAEV 360
           + +L  ALN + G+ CL  +G FY F   + AI   ++      S+D+ F   +L  A V
Sbjct: 303 HDWLVEALNKLPGVECLNGDGTFYVFPSFQGAIDADSSV-----STDVEFAEKLLTDAGV 357

Query: 361 AAVPGSAFGCEGYMRLSFATSMDNLQEAVKRIASLL 396
           A VPGSAFGC G+MRLSFATSM+NL++AV+R+   L
Sbjct: 358 ALVPGSAFGCPGHMRLSFATSMENLEKAVERLQKAL 393


Lambda     K      H
   0.318    0.133    0.380 

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: 439
Number of extensions: 9
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: 397
Length of database: 394
Length adjustment: 31
Effective length of query: 366
Effective length of database: 363
Effective search space:   132858
Effective search space used:   132858
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 paper from 2022 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