GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Sinorhizobium meliloti 1021

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate SMc01976 SMc01976 hypothetical protein

Query= BRENDA::Q5H4T8
         (397 letters)



>FitnessBrowser__Smeli:SMc01976
          Length = 390

 Score =  231 bits (589), Expect = 3e-65
 Identities = 144/369 (39%), Positives = 213/369 (57%), Gaps = 18/369 (4%)

Query: 34  AVMPPIYATSTYA--------QSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAF 85
           AV+PPI  TS +          S  GE     Y+R  NPT   +E  +A LEG   A  F
Sbjct: 25  AVVPPIVQTSLFTFKDYDEMVASYRGERVRPIYTRGLNPTVRHFEEMLAKLEGAEDAIGF 84

Query: 86  ASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKA 144
           ASGM+A +STV+  ++ G  +VA+  +Y   FRLF    +R   ++ ++VD  D  A   
Sbjct: 85  ASGMSAISSTVLSFVEPGDRIVAVKHVYPDAFRLFGTHLKRMR-VEVTYVDGRDEEAVAK 143

Query: 145 AIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLV 204
           A+    K+ ++E+PT+ ++   D+AA+A +AR+ G++TV+DN++ASP+ Q+P+SLG DLV
Sbjct: 144 ALPG-AKLFYMESPTSWVMDTHDVAALAALARRQGIVTVIDNSWASPVFQQPVSLGVDLV 202

Query: 205 VHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLR 264
           +HSA+KYL GHSD+V G+ V G    +    +     +GG   PFD++L +RG++TLP+R
Sbjct: 203 IHSASKYLGGHSDVVAGV-VAGSGELIGRIRSEAYPYLGGKLSPFDAWLLIRGMRTLPVR 261

Query: 265 MRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAA 324
           M+AH  +ALA+A+ L  HP +E V +PGL +H         +SG  G+ S + + G D  
Sbjct: 262 MKAHERSALAVARRLAEHPLVETVCHPGLGNH-----LPPGLSGTSGLFSFIFREGVD-V 315

Query: 325 KRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGD 384
           +RF +  +LF L  S GG ESL+    V+             GIS   VRL VG+E    
Sbjct: 316 RRFADHLKLFKLGVSWGGHESLIVPGEVVLAQKAEPNSAAAFGISPRSVRLHVGLEGTEA 375

Query: 385 LRGDLERAL 393
           L  DLE A+
Sbjct: 376 LWSDLEAAM 384


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: 418
Number of extensions: 26
Number of successful extensions: 6
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: 390
Length adjustment: 31
Effective length of query: 366
Effective length of database: 359
Effective search space:   131394
Effective search space used:   131394
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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