GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Klebsiella michiganensis M5al

Align L-asparaginase 1; L-asparaginase I; L-ASNase I; L-asparagine amidohydrolase I; EC 3.5.1.1 (characterized)
to candidate BWI76_RS11580 BWI76_RS11580 L-asparaginase 1

Query= SwissProt::P0A962
         (338 letters)



>FitnessBrowser__Koxy:BWI76_RS11580
          Length = 338

 Score =  624 bits (1610), Expect = 0.0
 Identities = 308/338 (91%), Positives = 318/338 (94%)

Query: 1   MQKKSIYVAYTGGTIGMQRSEQGYIPVSGHLQRQLALMPEFHRPEMPDFTIHEYTPLMDS 60
           MQKKSIYVAYTGGTIGMQRSE GYIPVSGHLQRQLALMPEFHRPEMPDFTIHEY PLMDS
Sbjct: 1   MQKKSIYVAYTGGTIGMQRSEHGYIPVSGHLQRQLALMPEFHRPEMPDFTIHEYAPLMDS 60

Query: 61  SDMTPEDWQHIAEDIKAHYDDYDGFVILHGTDTMAYTASALSFMLENLGKPVIVTGSQIP 120
           SDMTPEDWQHIA+DI+ HYD YDGFVILHGTDTMA+TASALSFMLENLGKPVIVTGSQIP
Sbjct: 61  SDMTPEDWQHIADDIRDHYDQYDGFVILHGTDTMAFTASALSFMLENLGKPVIVTGSQIP 120

Query: 121 LAELRSDGQINLLNALYVAANYPINEVTLFFNNRLYRGNRTTKAHADGFDAFASPNLPPL 180
           LAELRSDGQINLLNALYVAANYPINEV+LFFNNRLYRGNRTTKAHADGF+AFASPNL PL
Sbjct: 121 LAELRSDGQINLLNALYVAANYPINEVSLFFNNRLYRGNRTTKAHADGFNAFASPNLAPL 180

Query: 181 LEAGIHIRRLNTPPAPHGEGELIVHPITPQPIGVVTIYPGISADVVRNFLRQPVKALILR 240
           LEAGIHIRRL TPPAPHG GEL+VHPITPQPIGVVTIYPGISADVVRNFLRQPVKALILR
Sbjct: 181 LEAGIHIRRLGTPPAPHGSGELVVHPITPQPIGVVTIYPGISADVVRNFLRQPVKALILR 240

Query: 241 SYGVGNAPQNKAFLQELQEASDRGIVVVNLTQCMSGKVNMGGYATGNALAHAGVIGGADM 300
           SYGVGNAPQN  F+Q L EAS RGIVVVNLTQCMSGKVNMGGYATGNALA AGVI G DM
Sbjct: 241 SYGVGNAPQNGEFIQVLTEASQRGIVVVNLTQCMSGKVNMGGYATGNALAQAGVISGFDM 300

Query: 301 TVEATLTKLHYLLSQELDTETIRKAMSQNLRGELTPDD 338
           TVEATLTKLHYLLSQ+LD   IR AM +NLRGELTPD+
Sbjct: 301 TVEATLTKLHYLLSQDLDVAAIRHAMQENLRGELTPDE 338


Lambda     K      H
   0.318    0.136    0.398 

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: 572
Number of extensions: 12
Number of successful extensions: 1
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: 338
Length of database: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
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: 49 (23.5 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