Alignments for a candidate for ans in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for ans in Klebsiella michiganensis M5al

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate BWI76_RS08180 BWI76_RS08180 asparagine synthase B

Query= BRENDA::P22106
         (554 letters)



>FitnessBrowser__Koxy:BWI76_RS08180
          Length = 553

 Score = 1074 bits (2777), Expect = 0.0
 Identities = 520/553 (94%), Positives = 538/553 (97%)

Query: 1   MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60
           MCSIFGV DIKTDA ELRKKALELSRLMRHRGPDWSG+YA D AILAHERLSIVDVNAGA
Sbjct: 1   MCSIFGVLDIKTDAGELRKKALELSRLMRHRGPDWSGVYACDKAILAHERLSIVDVNAGA 60

Query: 61  QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120
           QPLYN  KTH LAVNGEIYNHQALRAEYGDRY FQTGSDCEVILALYQEKGP+FLDDLQG
Sbjct: 61  QPLYNAAKTHALAVNGEIYNHQALRAEYGDRYAFQTGSDCEVILALYQEKGPDFLDDLQG 120

Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180
           MFAFALYDSEKDAYLIGRDH+GIIPLYMG+DEHG  YVASEMKALVPVCRTIKEFPAGSY
Sbjct: 121 MFAFALYDSEKDAYLIGRDHIGIIPLYMGHDEHGNFYVASEMKALVPVCRTIKEFPAGSY 180

Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240
           LWS+DGEIR YY RDWFDYDAVKDNVTDKNELRQALE+SVKSHLMSDVPYGVLLSGGLDS
Sbjct: 181 LWSKDGEIREYYQRDWFDYDAVKDNVTDKNELRQALEESVKSHLMSDVPYGVLLSGGLDS 240

Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300
           S+ISAITKKYAARRVEDQE+SEAWWPQLHSFAVGL G+PDLKAAQEVANHLGTVHHEIHF
Sbjct: 241 SVISAITKKYAARRVEDQEKSEAWWPQLHSFAVGLEGAPDLKAAQEVANHLGTVHHEIHF 300

Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360
           TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY
Sbjct: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360

Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420
           FHKAPNAKELHEETVRKL ALHM+DCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD
Sbjct: 361 FHKAPNAKELHEETVRKLQALHMFDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420

Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480
           KMCGNGKMEKH+LRECFE+YLPASVAWRQKEQFSDGVGYSWIDTLKEVAA+Q+SDQQLET
Sbjct: 421 KMCGNGKMEKHVLRECFESYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAEQISDQQLET 480

Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540
           A FRFPYNTP+SKEAYLYREIFEELFP+PSAAECVPGGPSVACSSAKAIEWDE+FKKM+D
Sbjct: 481 ASFRFPYNTPSSKEAYLYREIFEELFPVPSAAECVPGGPSVACSSAKAIEWDESFKKMND 540

Query: 541 PSGRAVGVHQSAY 553
           PSGRAVGVHQSAY
Sbjct: 541 PSGRAVGVHQSAY 553


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: 1145
Number of extensions: 25
Number of successful extensions: 1
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: 553
Length adjustment: 36
Effective length of query: 518
Effective length of database: 517
Effective search space:   267806
Effective search space used:   267806
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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

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