Alignments for a candidate for ans in Methylomonas methanica MC09

GapMind for catabolism of small carbon sources

Alignments for a candidate for ans in Methylomonas methanica MC09

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate WP_013817859.1 METME_RS05875 asparagine synthase (glutamine-hydrolyzing)

Query= BRENDA::P22106
         (554 letters)



>NCBI__GCF_000214665.1:WP_013817859.1
          Length = 621

 Score =  144 bits (363), Expect = 1e-38
 Identities = 130/445 (29%), Positives = 190/445 (42%), Gaps = 77/445 (17%)

Query: 1   MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNA-G 59
           MC  F V+    D  +  +  +   R + HRGPD  G +   +  +   RLS++D++A G
Sbjct: 1   MCGFFAVYRPIADIKKFEEAIISAGRTLTHRGPDDEGSFCDGHFGVHFRRLSVIDLSASG 60

Query: 60  AQPLYNQQKTHVLAVNGEIYNHQALRAEYGDR-YQFQTGSDCEVILALYQEKGPEFLDDL 118
            QP+ +     VL  NGEIYN++ LR +  +R + F+  SD EV+LA + E G E ++ L
Sbjct: 61  HQPMLSADDRFVLVFNGEIYNYRDLRNKLIERNHNFRGDSDSEVLLAAFVEWGAECVNYL 120

Query: 119 QGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPV---------C 169
           +GMFAF ++D +       RD LGI PLY   D    L+ ASE+KA++           C
Sbjct: 121 RGMFAFLIWDRQSQILHAFRDRLGIKPLYYCRDGDTFLF-ASEIKAILSFAPHLAKPNQC 179

Query: 170 RTIKEFPAGSYLWSQDGEIRSY--------------------YHRDWFDYDAVKDNVTDK 209
              K    G   W  D E   +                     H  W    AV     ++
Sbjct: 180 AVFKFLARG---WVDDTEDTFFEGITSVAPGTVHRLERGNATKHLYWHPTFAV-GKPYEQ 235

Query: 210 NELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERS-------- 261
              R +   ++  HL SDVP    LSGG+DSS I A+  +  ++  E Q  S        
Sbjct: 236 ETFRNSFSQTISLHLQSDVPLAATLSGGMDSSSIVALAAQEVSQPEEIQAFSVIPPETVD 295

Query: 262 EAWWPQLHSFAVGLPGS---PDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIET 318
           E++W        G+  +   PD     EV + + T H E   +           IY    
Sbjct: 296 ESFWIDCTVIKTGIRHAYLQPDWSEMSEVFDTVLTAHDEPFQS--------SSCIY---- 343

Query: 319 YDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGG-------YLYFHKAPNAKELH 371
                       YL+ R++   GIK++L GEG DEV GG       YLY  +A    EL 
Sbjct: 344 -----------QYLLRREVAQRGIKVLLVGEGGDEVLGGYRRLFYPYLYALEADGRYELF 392

Query: 372 EETVRKLLALHMYDCARANKAMSAW 396
            + +    A    D A A   + A+
Sbjct: 393 NQALNGASAFLGIDRASALSQLKAY 417



 Score = 35.0 bits (79), Expect = 9e-06
 Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 395 AWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFEAYLPASVAWRQKEQFS 454
           A GVEARVPFLD +FL+     +  + M     + K +LR      LP  V  R+ +   
Sbjct: 491 AHGVEARVPFLDHRFLEQVFSFDYAEFMLHG--VNKSMLRRAMVGVLPEEVVGRRDKSPR 548

Query: 455 DGVGYSWI 462
            G    +I
Sbjct: 549 PGSNVHFI 556


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: 781
Number of extensions: 42
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 554
Length of database: 621
Length adjustment: 37
Effective length of query: 517
Effective length of database: 584
Effective search space:   301928
Effective search space used:   301928
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 2024 update 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

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 catabolism of small carbon sources