GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metB in Shewanella loihica PV-4

Align cystathionine γ-lyase (EC 2.5.1.48) (characterized)
to candidate 5210044 Shew_2491 methionine gamma-lyase (RefSeq)

Query= metacyc::HP0106-MONOMER
         (380 letters)



>FitnessBrowser__PV4:5210044
          Length = 391

 Score =  306 bits (784), Expect = 6e-88
 Identities = 169/387 (43%), Positives = 236/387 (60%), Gaps = 11/387 (2%)

Query: 2   RMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAI--------GRHKGYEYSRSGNPTRF 53
           ++ T++IH G  E    GA+  P+ Q++T+  + +        G  +GY Y+R GNPT  
Sbjct: 6   KLATQVIHAG-HEANQHGALVSPLVQSATFTFETVEQGGDCFAGEQQGYIYTRLGNPTTA 64

Query: 54  ALEELIADLEGGVKGFAFASGLAGIHA-VFSLLQSGDHVLLGDDVYGGTFRLFNQVLVKN 112
            LE  +A LEG     A ASG+A + A + + L  GDH++    VYG TF L  +   + 
Sbjct: 65  ELERKMAVLEGSEAAAATASGMAAVSAALLTNLSQGDHLVASKAVYGCTFALMTEQFKRF 124

Query: 113 GLSCTIIDTSDISQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNT 172
           G+  T++D  +++ I +AI+PNTKAL+ ETP NP L + DLA  A++AK H L++IVDNT
Sbjct: 125 GIEVTLVDFCEVANIAQAIRPNTKALFCETPVNPHLDVYDLAAIAALAKRHQLVSIVDNT 184

Query: 173 FATPYYQNPLLLGADIVAHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGP 232
           F TP  Q PL +G D+V HS TKYL GH DV+AG+V    E + +        IGGV+ P
Sbjct: 185 FMTPLLQRPLSMGIDMVIHSATKYLNGHGDVIAGIVCGTEEMITKVKLEVLKDIGGVISP 244

Query: 233 QDSWLLQRGIKTLGLRMEAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRG 292
            D+WL+ RG+KTL +R+  H  NA  VAE+L++HP+V RVYYPGL  H  + L  KQM  
Sbjct: 245 HDAWLILRGLKTLDVRLARHCDNAERVAEYLQQHPQVARVYYPGLKGHSGHALLGKQMLR 304

Query: 293 FSGMLSFTLKNDSEAV-AFVESLKLFILGESLGGVESLVGIPAFMTHACIPKTQREAAGI 351
             G+++F LK   +A  AF   LKLF +  SLG  ESL+  PA MTH+      R  AGI
Sbjct: 305 AGGVVAFELKGSFDAAKAFANRLKLFKIAVSLGDAESLIQHPASMTHSPYSPEARMDAGI 364

Query: 352 RDGLVRLSVGIEHEQDLLEDLEQAFAK 378
            D L+R+S+G+E   D++ DL QAF +
Sbjct: 365 GDSLLRISLGLEDSDDIIADLAQAFGE 391


Lambda     K      H
   0.319    0.137    0.394 

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: 377
Number of extensions: 15
Number of successful extensions: 3
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: 380
Length of database: 391
Length adjustment: 30
Effective length of query: 350
Effective length of database: 361
Effective search space:   126350
Effective search space used:   126350
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

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:

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