GapMind for Amino acid biosynthesis

 

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

Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate AO356_24030 AO356_24030 sulfurtransferase

Query= curated2:Q1M0P5
         (380 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_24030
          Length = 921

 Score =  226 bits (577), Expect = 2e-63
 Identities = 142/390 (36%), Positives = 213/390 (54%), Gaps = 22/390 (5%)

Query: 3   MQTKLIHGG-ISEDATTGAVSVPIYQTSTYRQDAIGHHKG----------YEYSRSGNPT 51
           ++T L+HG   ++      V+VP+ + ST   D +   +             Y   GNPT
Sbjct: 532 LRTHLVHGARTAKGVGARPVNVPVSRLSTVLFDNLAQMRDARARRDSERVLSYGARGNPT 591

Query: 52  RFALEELIADLEGGVKGFAFASGLAGIHAVF-SLLQSGDHVLLGDDVYGGTFRLFNKVLV 110
            FALE+L+ +LEGG +   F +GLA +   F + L+ GDHVL+ D VY    R+    L 
Sbjct: 592 AFALEDLVTELEGGYRTRLFGTGLAAVAQTFLAYLRPGDHVLITDAVYAPVRRVARDFLE 651

Query: 111 KNGLSCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVD 170
             G+        D S +   ++ NTK +Y E P + L ++ DL   A++ K  G+L  VD
Sbjct: 652 AFGIEVDYF-APDGSDLPGRLQANTKMVYTEVPGSLLYELCDLPAIAALCKPRGILLAVD 710

Query: 171 NTFATPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVL 230
           NT+       PL LGADI + + TKYL GHSDVV G V T  EA    +A   +  G  +
Sbjct: 711 NTWGAGVLYRPLALGADISIMALTKYLSGHSDVVMGSVCTRQEAW-PALAAMSDTFGNTV 769

Query: 231 GPQDSWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQM 290
            P D++L+ RG +TL  R+  H++ AL +A +L+  P+V+RV++P LP HP + L ++  
Sbjct: 770 SPDDAYLVLRGARTLVPRLDTHERQALEIAHWLQAQPQVKRVFHPALPEHPGHGLWQRDF 829

Query: 291 RGFSGMLSFTLK--NDSEATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREA 348
            G +G+LSF L+  +D+    F+++L++F LG S GG ESLV      T A     QR  
Sbjct: 830 NGSNGLLSFELREHDDAYLERFIDALQVFGLGASWGGFESLV------TVADTQDRQRAE 883

Query: 349 AGIRDGLVRLSVGIEHEQDLLEDLEQAFAK 378
               + +VRL VG+E  + L+EDL + FA+
Sbjct: 884 DRALNPVVRLHVGLEDVEVLIEDLRRGFAQ 913


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: 770
Number of extensions: 35
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: 380
Length of database: 921
Length adjustment: 37
Effective length of query: 343
Effective length of database: 884
Effective search space:   303212
Effective search space used:   303212
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: 53 (25.0 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