GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Mesorhizobium ciceri WSM1271

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate YP_004144523.1 Mesci_5375 asparagine synthase

Query= BRENDA::P22106
         (554 letters)



>NCBI__GCF_000185905.1:YP_004144523.1
          Length = 673

 Score =  166 bits (419), Expect = 3e-45
 Identities = 128/411 (31%), Positives = 200/411 (48%), Gaps = 71/411 (17%)

Query: 1   MCSIFGVFDIKTDAVELRKKAL-ELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAG 59
           MC I G+  +   A    + AL  ++  + HRGPD SG+Y    A LAH RLS++D++ G
Sbjct: 1   MCGIAGIVALNAAAEPPSRAALLRMAAALSHRGPDESGVYRDRRAGLAHTRLSVIDLSTG 60

Query: 60  AQPLYNQQKTHVLAVNGEIYNHQALRAE-YGDRYQFQTGSDCEVILALYQEKGPEFLDDL 118
            QPL +   T  +  NGEI+N+  LR +     ++F+T SD EVI+  Y+  G    + L
Sbjct: 61  QQPLADTGDTTWIVFNGEIFNYVELREQLMALGHRFRTRSDTEVIVHAYRAWGVAAFERL 120

Query: 119 QGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKAL------------- 165
            G +A A++DS     ++ RD  GI PL++  +  G+L+ ASE+KA+             
Sbjct: 121 NGQWALAIWDSLTGRLVLSRDRFGICPLHL-CEHAGRLHFASEVKAIFAADPAIPRAFDP 179

Query: 166 ------------VP---VCRTIKEFPAGSYLWSQDGEIRSYYHRDWFD-YDAVKDNVTDK 209
                       VP   V + +KE   G      +G +R   H  W   Y  + D     
Sbjct: 180 AGIDQTFTLWTVVPPQGVFQGVKELTPGHVRIYDNGSVRE--HAFWKPCYPEIADQAHGT 237

Query: 210 ---------NELRQALEDSVKSHLM-SDVPYGVLLSGGLDSSIISAITKKYA-------A 252
                    +E+R AL+ +    ++ +DVP G  LSGGLDSS+++ + +++A       +
Sbjct: 238 FTGSLDDAVDEVRSALQAATALRMVKADVPVGCYLSGGLDSSLVAMLGRRFAGAPFQTFS 297

Query: 253 RRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDV 312
            R  D E  E  + +L                  VA+  G  HHE+  +  +  +   DV
Sbjct: 298 LRFADAEYDETRYQRL------------------VASASGGEHHEVMVSRGDIAEVFPDV 339

Query: 313 IYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHK 363
           I H E   + T  A  P++L+SR ++  GIK+VL+GEG+DE+F GY  F +
Sbjct: 340 IRHAERPILRT--APAPLFLLSRLVREHGIKVVLTGEGADEMFAGYDLFRE 388



 Score = 38.9 bits (89), Expect = 6e-07
 Identities = 25/89 (28%), Positives = 51/89 (57%), Gaps = 4/89 (4%)

Query: 365 PNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCG 424
           P A++ + E +R L++ ++   ++ ++ + A  VE R PFLD + + +A  + P  K+  
Sbjct: 488 PLAQDQYLE-IRTLMSGYLLS-SQGDRMLMAHSVEGRFPFLDDRLVALANSLPPDYKL-- 543

Query: 425 NGKMEKHILRECFEAYLPASVAWRQKEQF 453
               EKH+L+   ++ +PA V  R+K+ +
Sbjct: 544 RILDEKHVLKRVAKSIVPAEVVARKKQPY 572


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: 788
Number of extensions: 49
Number of successful extensions: 6
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: 673
Length adjustment: 37
Effective length of query: 517
Effective length of database: 636
Effective search space:   328812
Effective search space used:   328812
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 24 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