GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ans in Dyella japonica UNC79MFTsu3.2

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate N515DRAFT_1546 N515DRAFT_1546 asparagine synthase (glutamine-hydrolysing)

Query= BRENDA::P22106
         (554 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1546 N515DRAFT_1546
           asparagine synthase (glutamine-hydrolysing)
          Length = 559

 Score =  674 bits (1739), Expect = 0.0
 Identities = 340/560 (60%), Positives = 412/560 (73%), Gaps = 10/560 (1%)

Query: 1   MCSIFGVFDIKT--DAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNA 58
           MCSIFG+FD++   D   LR++ALELS+  RHRGPDWSG++     IL HERL+IVD  +
Sbjct: 1   MCSIFGMFDLQPGDDLAGLRRQALELSQRQRHRGPDWSGVFVDAGVILVHERLAIVDPAS 60

Query: 59  GAQPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEF---- 114
           G+QPL ++++T  LAVNGEIYNH+ LRA  G  Y F TGSDCEVI ALY+E GPE     
Sbjct: 61  GSQPLRSREETLALAVNGEIYNHRELRAASG--YDFTTGSDCEVINALYRELGPEEFLAR 118

Query: 115 -LDDLQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIK 173
            +  L G+FAFAL+DS    YLI RD +G+ PLY G+D  G+L VASEMKALV VC  + 
Sbjct: 119 GIKQLNGIFAFALWDSATQRYLIARDPIGVCPLYWGHDGEGRLCVASEMKALVGVCADVS 178

Query: 174 EFPAGSYLWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVL 233
            FP G    S  GE+  YY + W  Y+       + + LR A E +V   LM+DVPYGVL
Sbjct: 179 AFPPGHVYDSATGEVTRYYRKHWRSYEVTHGQQLEPSALRGAFEQAVHRQLMTDVPYGVL 238

Query: 234 LSGGLDSSIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGT 293
           LSGGLDSS+++A   ++A  R+ED +RSEAWWP+LHSFA+GL GSPDL AAQ  A+ LGT
Sbjct: 239 LSGGLDSSLVAACAARFARERIEDDDRSEAWWPRLHSFAIGLEGSPDLAAAQVAADALGT 298

Query: 294 VHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDE 353
           VHH   +T  EGLDA+ +VI HIETYDVTTIRASTPM+L++R+IKAMG+KMVLSGEGSDE
Sbjct: 299 VHHGFVYTFWEGLDALPEVIRHIETYDVTTIRASTPMFLLARRIKAMGVKMVLSGEGSDE 358

Query: 354 VFGGYLYFHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVA 413
           +FGGYLYFHKAP+ +  HEETVRKL ALH +DC RANKAM AWGVEARVPFLD +FLDVA
Sbjct: 359 IFGGYLYFHKAPSPEAFHEETVRKLDALHSFDCLRANKAMMAWGVEARVPFLDLEFLDVA 418

Query: 414 MRINPQDKMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQV 473
           M ++ + KM G+G++EK +LRE F+  LP S+ WRQKEQFSDGVGY WID LK  A Q V
Sbjct: 419 MGLDARYKMAGHGRIEKAVLREAFQGALPDSILWRQKEQFSDGVGYGWIDGLKAHAEQVV 478

Query: 474 SDQQLETARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDE 533
           SD++   A  RFP+N P +KEAYLYR IFE+ FP  + A  VPGG S+ACSS  A+ WD 
Sbjct: 479 SDREFAAASTRFPHNPPATKEAYLYRRIFEQHFPGEACAATVPGGKSIACSSPAALAWDP 538

Query: 534 AFKKMDDPSGRAV-GVHQSA 552
           AF    DPSGRAV GVHQ A
Sbjct: 539 AFAAAADPSGRAVRGVHQQA 558


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: 919
Number of extensions: 24
Number of successful extensions: 4
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: 559
Length adjustment: 36
Effective length of query: 518
Effective length of database: 523
Effective search space:   270914
Effective search space used:   270914
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 preprint 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