GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Pseudomonas fluorescens FW300-N2C3

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate AO356_21470 AO356_21470 O-succinylhomoserine sulfhydrylase

Query= BRENDA::Q5H4T8
         (397 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_21470
          Length = 403

 Score =  315 bits (807), Expect = 1e-90
 Identities = 175/386 (45%), Positives = 249/386 (64%), Gaps = 17/386 (4%)

Query: 19  TLAIHGGQ--SPDPSTGAVMPPIYATSTY--------AQSSPGEHQGFEYSRTHNPTRFA 68
           TLA+  GQ  +P+   G    P++ TS+Y        A    GE  G  YSR  NPT  A
Sbjct: 21  TLAVRAGQHRTPEAEHG---DPMFFTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRA 77

Query: 69  YERCVAALEGGTRAFAFASGMAAT-STVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTA 127
           +E  +AALEG  +A A A+GMAA  + VM L  AG HV+    ++G T  LFE+  +R  
Sbjct: 78  FEERIAALEGAEQAVATATGMAAIMAVVMSLCSAGDHVLVSRSVFGSTISLFEKYFKRF- 136

Query: 128 GLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNT 187
           G++  +V L D +A+ AAI+A+TK++++E+P+NP+ +LVDIAA+A IA   G + VVDN 
Sbjct: 137 GVEVDYVPLADLSAWDAAIKANTKLLFVESPSNPLAELVDIAALAEIAHAKGAMLVVDNC 196

Query: 188 FASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQG 247
           F +P LQ+PL LGAD+VVHSATK+++G    +GG+ V G   ++ E + FL+ + G    
Sbjct: 197 FCTPALQQPLKLGADVVVHSATKFIDGQGRCMGGV-VAGRGEQMKEVVGFLRTA-GPTLS 254

Query: 248 PFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMS 307
           PF++++ L+GL+TL LRM+AHC NA ALA+WLE    IEKV Y GL SHPQH LA RQ  
Sbjct: 255 PFNAWIFLKGLETLGLRMKAHCANAQALAEWLEQQDGIEKVHYAGLKSHPQHDLALRQQR 314

Query: 308 GFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLG 367
           GFG +VS  +KGG + A RF + T L ++  +LG  ++ + HP+  +H  +    RE  G
Sbjct: 315 GFGAVVSFEVKGGKEGAWRFIDATRLISITANLGDSKTTITHPSTTSHGRLSPQERESAG 374

Query: 368 ISDALVRLSVGIEDLGDLRGDLERAL 393
           I D+L+R++VG+ED+ DL+ DL R L
Sbjct: 375 IRDSLIRVAVGLEDIADLQADLARGL 400


Lambda     K      H
   0.320    0.134    0.391 

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: 439
Number of extensions: 26
Number of successful extensions: 4
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: 397
Length of database: 403
Length adjustment: 31
Effective length of query: 366
Effective length of database: 372
Effective search space:   136152
Effective search space used:   136152
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.

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