GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ans in Shewanella sp. ANA-3

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate 7025394 Shewana3_2549 asparagine synthetase B (RefSeq)

Query= BRENDA::P22106
         (554 letters)



>lcl|FitnessBrowser__ANA3:7025394 Shewana3_2549 asparagine
           synthetase B (RefSeq)
          Length = 554

 Score =  808 bits (2088), Expect = 0.0
 Identities = 392/554 (70%), Positives = 461/554 (83%), Gaps = 1/554 (0%)

Query: 1   MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60
           MCSIF + DI++DA ELR+ ALE+S+LMRHRGPDWSGIYASD AILAHERL+IVD+  GA
Sbjct: 1   MCSIFSILDIQSDAKELRQVALEMSKLMRHRGPDWSGIYASDKAILAHERLAIVDIEHGA 60

Query: 61  QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120
           QPL  +  + +LAVNGEIYNH+ L+A+ GD+Y +QT SDCEVILALYQE G EFLD L G
Sbjct: 61  QPLLTEDGSLILAVNGEIYNHKELKAQLGDKYSYQTNSDCEVILALYQEYGTEFLDKLNG 120

Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180
           +FAF LYD  KDAYLIGRDH+GIIPLY G D  G  YVASEMKAL+PVC+T+ EF  G Y
Sbjct: 121 IFAFVLYDKAKDAYLIGRDHMGIIPLYTGRDAAGNFYVASEMKALMPVCKTVAEFQPGQY 180

Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240
           L+S  GE   YY RDW  +DAVKDN   + ELR ALE +VK  LMSDVPYGVLLSGGLDS
Sbjct: 181 LYSSIGEPVQYYTRDWQSFDAVKDNGASQEELRDALEAAVKRQLMSDVPYGVLLSGGLDS 240

Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300
           S+ISAIT+ +A RR+ED ++S AWWPQLHSFAVGL G+PDL AA++VA+ +GT+HHEI+F
Sbjct: 241 SVISAITQTFAKRRIEDDDQSGAWWPQLHSFAVGLKGAPDLAAAKKVADAIGTIHHEINF 300

Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360
           T QEGLDAI++VIYH+ETYDVTTIRA+TPMYLM+RKIKAMGIKMVLSGEG+DE+FGGYLY
Sbjct: 301 TFQEGLDAIKEVIYHLETYDVTTIRAATPMYLMARKIKAMGIKMVLSGEGADELFGGYLY 360

Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420
           FHKAPNA+  HEE VRKL  LH++DC RANKAM+AWG+EARVPFLDK+F+DVAMRINP+ 
Sbjct: 361 FHKAPNAQAFHEELVRKLDKLHLFDCLRANKAMAAWGLEARVPFLDKEFMDVAMRINPEA 420

Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480
           KM  +G++EKHILR+ FE  LP  VAWRQKEQFSDGVGYSWID LK  AA+QV D QL  
Sbjct: 421 KMSKDGRIEKHILRQAFEHKLPKEVAWRQKEQFSDGVGYSWIDGLKAHAAEQVDDLQLAN 480

Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540
           A+FRFPYNTP +KEAY YR  FEE +PLPSAAE VPGG SVACS+ +A+ WDE+ + + D
Sbjct: 481 AKFRFPYNTPETKEAYFYRCFFEEHYPLPSAAETVPGGKSVACSTPEALAWDESLRGIID 540

Query: 541 PSGRAV-GVHQSAY 553
           PSGRAV  VH ++Y
Sbjct: 541 PSGRAVRSVHAASY 554


Lambda     K      H
   0.319    0.135    0.407 

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: 916
Number of extensions: 27
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: 554
Length of database: 554
Length adjustment: 36
Effective length of query: 518
Effective length of database: 518
Effective search space:   268324
Effective search space used:   268324
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 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