GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metB in Sinorhizobium meliloti 1021

Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate SMc01976 SMc01976 hypothetical protein

Query= curated2:Q1M0P5
         (380 letters)



>FitnessBrowser__Smeli:SMc01976
          Length = 390

 Score =  233 bits (593), Expect = 9e-66
 Identities = 144/371 (38%), Positives = 212/371 (57%), Gaps = 17/371 (4%)

Query: 20  AVSVPIYQTSTYR----QDAIGHHKGYE----YSRSGNPTRFALEELIADLEGGVKGFAF 71
           AV  PI QTS +      + +  ++G      Y+R  NPT    EE++A LEG      F
Sbjct: 25  AVVPPIVQTSLFTFKDYDEMVASYRGERVRPIYTRGLNPTVRHFEEMLAKLEGAEDAIGF 84

Query: 72  ASGLAGIHA-VFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLSCTIIDTSDLSQIKKA 130
           ASG++ I + V S ++ GD ++    VY   FRLF   L +  +  T +D  D   + KA
Sbjct: 85  ASGMSAISSTVLSFVEPGDRIVAVKHVYPDAFRLFGTHLKRMRVEVTYVDGRDEEAVAKA 144

Query: 131 IKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQNPLLLGADIVV 190
           + P  K  Y+E+P++ ++   D+A  A++A+  G++T++DN++A+P +Q P+ LG D+V+
Sbjct: 145 L-PGAKLFYMESPTSWVMDTHDVAALAALARRQGIVTVIDNSWASPVFQQPVSLGVDLVI 203

Query: 191 HSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQRGIKTLGLRMQ 250
           HS +KYLGGHSDVVAG+V  + E + +  +     +GG L P D+WLL RG++TL +RM+
Sbjct: 204 HSASKYLGGHSDVVAGVVAGSGELIGRIRSEAYPYLGGKLSPFDAWLLIRGMRTLPVRMK 263

Query: 251 AHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFTLKNDSEATPF 310
           AH+++AL VA  L +HP VE V +PGL  H         + G SG+ SF  +   +   F
Sbjct: 264 AHERSALAVARRLAEHPLVETVCHPGLGNH-----LPPGLSGTSGLFSFIFREGVDVRRF 318

Query: 311 VESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAA-GIRDGLVRLSVGIEHEQDLL 369
            + LKLF LG S GG ESL+ VP  +  A   +    AA GI    VRL VG+E  + L 
Sbjct: 319 ADHLKLFKLGVSWGGHESLI-VPGEVVLAQKAEPNSAAAFGISPRSVRLHVGLEGTEALW 377

Query: 370 EDLEQAFAKIS 380
            DLE A    S
Sbjct: 378 SDLEAAMTAAS 388


Lambda     K      H
   0.318    0.136    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: 359
Number of extensions: 16
Number of successful extensions: 5
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: 390
Length adjustment: 30
Effective length of query: 350
Effective length of database: 360
Effective search space:   126000
Effective search space used:   126000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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