Alignments for a candidate for asnB in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Methanosarcina acetivorans C2A

Align Putative asparagine synthetase [glutamine-hydrolyzing] 1; EC 6.3.5.4 (uncharacterized)
to candidate WP_011021961.1 MA_RS10245 asparagine synthetase B

Query= curated2:Q58516
         (541 letters)



>NCBI__GCF_000007345.1:WP_011021961.1
          Length = 497

 Score =  234 bits (598), Expect = 4e-66
 Identities = 190/550 (34%), Positives = 273/550 (49%), Gaps = 100/550 (18%)

Query: 1   MCSISGII-VKDNQISAKYSIDMMKILKHRGRDNSGLLLDDEVIYFNDFEDVEDLEEEMI 59
           MC I+G+    D+ +  K    M+  L HRG D  G+                       
Sbjct: 1   MCGIAGVFGTPDSNLKVK---KMLAALGHRGPDACGI--------------------HTA 37

Query: 60  GNLSLAHNRLAIVGRYGVQPIPNEDETIWLVCNGEIYNYIELREYLKQNHEFRTDSDNEV 119
           G+LS+ +  L I G    QP+  +     LV NGEI+N+ EL   +      + DSD E+
Sbjct: 38  GDLSIGNTLLKITGDMP-QPLTGKGA---LVLNGEIFNFRELAAEIG----IKIDSDTEL 89

Query: 120 IIHLYEE-------------EKLEELDGDYAFAIYDKSKNVVRLARDMFGVKPLFYVDRD 166
           +  L E                L +++GDYA A     + V  LARD  GVKPLFY    
Sbjct: 90  LFSLIETGVKEGSTPIDAVCSALSKVNGDYALAYACGGELV--LARDPSGVKPLFYCSGT 147

Query: 167 K----YFAFASERKALWHLLINIDGCERDLDELNSKIKTLKPNSQLIYYLDDNRF--EII 220
           +      AFASE+KAL  +              + K K       L +  +  +   +I 
Sbjct: 148 EGEKPEIAFASEKKALAFI--------------SRKAKPFPQGGILGFNTESGKITEKIP 193

Query: 221 EGFKKLELNYMKERSY--EEAKEYLDRALKNSVLKRVRGLDKVGIICSGGVDSSLIAKLA 278
           EG+  LE+   ++R Y   EA   L   L+ +V   +R     GI  SGG+DS+ +A LA
Sbjct: 194 EGY--LEIKSPEKRIYTEHEALSQLKETLEKAV--ELRLTPTTGIAFSGGIDSTFLAALA 249

Query: 279 S-LYCEVILYAVGTENSEDLIYAERLAKDLNLKLRKKI--ISEEEYEEYVFKVAKAIDEV 335
             +   V LYAVG  +S D+  AER A+ + ++   K+  +S EE E  V +V  A +  
Sbjct: 250 KRIDPGVSLYAVGLPDSHDITQAERAAEAIGMRKNLKVHFLSPEEIEAAVPRVVYATEST 309

Query: 336 DLMKIGVGIPIYVASEMANEDGLKVVLSGQGADELFGGYARHERIYRERGEEELKKELLK 395
           D M + +GIP+Y+ ++ A EDG +V+L+GQGADELFGGY RHE  + ++G E L +E+  
Sbjct: 310 DPMTVAIGIPLYIVAKTAKEDGKRVLLTGQGADELFGGYRRHEE-FLKKGAEVLDREIYS 368

Query: 396 DVYNLYKVNLERDDHCTMANGVELRVPFLDEEVVEIALSIPIEYKMSELSNRPYAESNIS 455
           D+  + K+NLERDD  TMAN VELRVPFLD+EV++  L+I  E K+  L    Y E    
Sbjct: 369 DLATISKINLERDDMVTMANSVELRVPFLDKEVIKTGLAIRPELKV--LKKDGYYEDGYY 426

Query: 456 LKSEPINGLKNTNLNIKCVRSVRKKILRDVASQYLPDYIAYRPKKAAQYGSGGEKMIYKV 515
                                 RK ILR  A   +P  I ++ KKA QYG+G +K++ ++
Sbjct: 427 ---------------------ERKYILRKAAKGLIPPEILWKEKKAMQYGTGVQKVLDRL 465

Query: 516 AKKYGFSKKR 525
           A+  GFSKK+
Sbjct: 466 ARDSGFSKKQ 475


Lambda     K      H
   0.318    0.138    0.388 

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: 640
Number of extensions: 45
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 541
Length of database: 497
Length adjustment: 35
Effective length of query: 506
Effective length of database: 462
Effective search space:   233772
Effective search space used:   233772
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis