GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Pseudomonas simiae WCS417

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate GFF3620 PS417_18530 O-succinylhomoserine sulfhydrylase

Query= SwissProt::P55218
         (403 letters)



>FitnessBrowser__WCS417:GFF3620
          Length = 403

 Score =  686 bits (1770), Expect = 0.0
 Identities = 335/403 (83%), Positives = 377/403 (93%)

Query: 1   MTQDWDAGRLDSDLEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAG 60
           M+Q+WDAGRLDSDL+G AFDTLAVRAGQ RTPEGEHG+ +F TSSYVFRTAADAAARFAG
Sbjct: 1   MSQEWDAGRLDSDLDGVAFDTLAVRAGQHRTPEGEHGDPMFFTSSYVFRTAADAAARFAG 60

Query: 61  EVPGNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRS 120
           EVPGNVYSRYTNPTVR FEERIAALEGAEQAVATA+GM+AILA+VMSLCS+GDHVLVSRS
Sbjct: 61  EVPGNVYSRYTNPTVRAFEERIAALEGAEQAVATATGMAAILAVVMSLCSAGDHVLVSRS 120

Query: 121 VFGSTISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAAL 180
           VFGSTISLF+KYFKRFGI+VDY PL+DL+ W+AA K NTKL FVESPSNPLAELVDIAAL
Sbjct: 121 VFGSTISLFEKYFKRFGIEVDYVPLADLSGWDAAIKANTKLLFVESPSNPLAELVDIAAL 180

Query: 181 AEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMK 240
           +E+AHAKGA+L VDNCFCTPALQQPLKLGAD+V+HSATK+IDGQGR MGGVVAGR EQMK
Sbjct: 181 SEVAHAKGAMLVVDNCFCTPALQQPLKLGADIVVHSATKFIDGQGRCMGGVVAGRSEQMK 240

Query: 241 EVVGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGL 300
           EVVGFLRTAGPTLSPFNAW+FLKGLETL +RM+AH A+A ALAEWLE+Q GIE+V+YAGL
Sbjct: 241 EVVGFLRTAGPTLSPFNAWIFLKGLETLSLRMKAHCANAQALAEWLEQQDGIEKVHYAGL 300

Query: 301 PSHPQHELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATT 360
            SHPQHELA+RQQ GFGAVVSF+VKGG++ AWRFIDATR++SIT NLGD+KTTI HP+TT
Sbjct: 301 KSHPQHELAQRQQRGFGAVVSFEVKGGKEGAWRFIDATRLISITANLGDSKTTITHPSTT 360

Query: 361 SHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403
           SHGRL+P++R  AGI DSLIR+AVGLED+ DL+AD+ARGLAAL
Sbjct: 361 SHGRLAPQEREAAGIRDSLIRIAVGLEDVADLQADLARGLAAL 403


Lambda     K      H
   0.319    0.133    0.392 

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: 568
Number of extensions: 12
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: 403
Length of database: 403
Length adjustment: 31
Effective length of query: 372
Effective length of database: 372
Effective search space:   138384
Effective search space used:   138384
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: 50 (23.9 bits)

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