GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Sphingomonas koreensis DSMZ 15582

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate Ga0059261_3119 Ga0059261_3119 asparagine synthase (glutamine-hydrolyzing)

Query= BRENDA::P22106
         (554 letters)



>FitnessBrowser__Korea:Ga0059261_3119
          Length = 616

 Score =  139 bits (351), Expect = 2e-37
 Identities = 121/374 (32%), Positives = 188/374 (50%), Gaps = 62/374 (16%)

Query: 28  MRHRGPDWSGIYASDNAI--LAHERLSIVDVNAGA-QPLYNQQKTHVLAVNGEIYNHQAL 84
           + HRGPD +G + S +    LA  RL+I+D++ G  QP++ +     +  NGEIYN + L
Sbjct: 26  LHHRGPDDTGQWWSPDGRVGLAQARLAIIDLSPGGHQPMHREADRLSVVFNGEIYNFRDL 85

Query: 85  RAEY-GDRYQFQTGSDCEVILALYQEKGPEFLDDLQGMFAFALYDSEKDAYLIGRDHLGI 143
           RAE  G  + F++ SD EV+LA Y + G   L  L GMFAFA++D+  +     RD  G 
Sbjct: 86  RAELEGLGHVFRSHSDTEVLLAAYAQWGIGCLTRLNGMFAFAIFDARANKVYFARDRAGE 145

Query: 144 IPLYMGYDEHGQLYVASEMKALVP---VCRTIKEFPAGSYLWSQ----DGEIRSYY---- 192
            PL+  +  +G ++ ASE+K L+    + R I       YL +     DG I + Y    
Sbjct: 146 KPLFY-HAANGTIHFASELKTLLADPTLPRVIDPAALDGYLLTGYVPGDGCILAGYRKLP 204

Query: 193 -------------HRDWF-----DYDAVKDNVTDK-NELRQALEDSVKSHLMSDVPYGVL 233
                        HR W      DY  V+D+      EL   LED+V   L++DVP GVL
Sbjct: 205 PGHAMELDLSSGAHRVWRYWNLPDYAPVEDDDAGLLGELEALLEDAVGRQLVADVPVGVL 264

Query: 234 LSGGLDSSIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGS---PDLKAAQEVANH 290
           LSGG+DSS+I+A+  + AA+              + +F +G  G+    +++ A+ +A+H
Sbjct: 265 LSGGVDSSLITAMAVRNAAK--------------VRTFTIGFAGAGPLNEIEHARLIADH 310

Query: 291 LGTVHHEI--HFTVQEGLDAIRDVIYHIETYDVTTIRAST-PMYLMSRKIKAMGIKMVLS 347
            GT   E+    TV E L  +         +D     +S  P +++S  ++     + L 
Sbjct: 311 FGTEQVELMAEPTVAELLPRL------AAQFDEPMADSSMFPTFMVSELVR-QHCTVALG 363

Query: 348 GEGSDEVFGGYLYF 361
           G+G DE+FGGY ++
Sbjct: 364 GDGGDELFGGYGHY 377



 Score = 26.2 bits (56), Expect = 0.004
 Identities = 19/97 (19%), Positives = 41/97 (42%), Gaps = 3/97 (3%)

Query: 360 YFHKAPNAKELHEETVRKLLALHMYD--CARANKAMSAWGVEARVPFLDKKFLDVAMRIN 417
           Y  + P   +L +   R     ++ +    + ++      +E R PFLD + ++ A    
Sbjct: 455 YRSRIPAMDDLLQRATRTDFGTYLSEDILVKVDRTSMLTSLEVRAPFLDHRLIEFAFGKV 514

Query: 418 PQDKMCGNGKMEKHILRECFEAYLPASVAWRQKEQFS 454
           P  ++      +K +L++     LP     ++K+ FS
Sbjct: 515 P-SRLKATASDKKILLKQLAARVLPPQFDRQRKQGFS 550


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: 745
Number of extensions: 39
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 554
Length of database: 616
Length adjustment: 36
Effective length of query: 518
Effective length of database: 580
Effective search space:   300440
Effective search space used:   300440
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:

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