GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Shewanella amazonensis SB2B

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate 6937968 Sama_2101 asparagine synthetase B (RefSeq)

Query= BRENDA::P22106
         (554 letters)



>FitnessBrowser__SB2B:6937968
          Length = 554

 Score =  795 bits (2053), Expect = 0.0
 Identities = 388/554 (70%), Positives = 451/554 (81%), Gaps = 1/554 (0%)

Query: 1   MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60
           MCSIF + DI++DA  +R+ ALE+S+L+RHRGPDWSGIYA D+A+LAHERL+IVD+  GA
Sbjct: 1   MCSIFAILDIQSDASAMRQVALEMSKLLRHRGPDWSGIYADDHAVLAHERLAIVDIEHGA 60

Query: 61  QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120
           QPL +   + VLAVNGEIYNH+ L+AE GD+Y +QT SDCEVILALYQE G +FLD L G
Sbjct: 61  QPLISDDGSLVLAVNGEIYNHKELKAELGDKYSYQTNSDCEVILALYQEYGSDFLDKLNG 120

Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180
           +FAF LYD  K  YLIGRDH+GIIPLY G D  G  YVASEMKALVPVC+T++ F  G Y
Sbjct: 121 IFAFVLYDKAKGTYLIGRDHIGIIPLYTGRDAKGNFYVASEMKALVPVCKTVETFAPGHY 180

Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240
           L S D +   YY RDW  +DAV DN     ELR ALE +VK  LMSDVPYGVLLSGGLDS
Sbjct: 181 LSSTDAQPVRYYQRDWQAFDAVVDNEASVEELRGALEAAVKRQLMSDVPYGVLLSGGLDS 240

Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300
           SI+SAIT+ +A RR+ED + SEAWWPQLHSFAVGL GSPDL A+++VA+ +GT+HHEIHF
Sbjct: 241 SIVSAITQTFAKRRIEDNDESEAWWPQLHSFAVGLKGSPDLAASRKVADAIGTIHHEIHF 300

Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360
           T QEGLDAI+DVIYH+ETYDVTTIRA+TPMYLM+RKIKAMGIKMVLSGEG+DE+FGGYLY
Sbjct: 301 TFQEGLDAIKDVIYHLETYDVTTIRAATPMYLMARKIKAMGIKMVLSGEGADELFGGYLY 360

Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420
           FHKAPN +  HEE VRKL  LH++DC RANKAM+AWG+EARVPFLDK+F+DVAMR+NP  
Sbjct: 361 FHKAPNPQAFHEELVRKLDKLHLFDCLRANKAMAAWGLEARVPFLDKEFMDVAMRLNPAA 420

Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480
           KM G GK+EKHILRE FE  LPA +AWRQKEQFSDGVGYSWID LKE AA QV D QL  
Sbjct: 421 KMSGKGKIEKHILREAFEHKLPAEIAWRQKEQFSDGVGYSWIDGLKEQAAAQVDDLQLAN 480

Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540
           ARFRFP+NTP +KEAY YR  FEELFPL SAA  VPGG SVACS+ +A+ WD + + + D
Sbjct: 481 ARFRFPHNTPETKEAYFYRCFFEELFPLESAALTVPGGKSVACSTPEALAWDASLQGIID 540

Query: 541 PSGRAV-GVHQSAY 553
           PSGRAV  VH  +Y
Sbjct: 541 PSGRAVREVHAQSY 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: 907
Number of extensions: 30
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.

Links

Downloads

Related tools

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