GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Methylocystis bryophila S285

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_085770261.1 B1812_RS02885 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= curated2:Q2G9T9
         (471 letters)



>NCBI__GCF_002117405.1:WP_085770261.1
          Length = 1018

 Score =  208 bits (530), Expect = 6e-58
 Identities = 163/478 (34%), Positives = 223/478 (46%), Gaps = 32/478 (6%)

Query: 9    HEPATGAEVWRGKVGDVEEV--------VARARRAWPAWAAQPLATRIELVRRFANEVRK 60
            H P  G      +VGDV E         +A A RA+ AW AQP  TR +++ R A  +  
Sbjct: 550  HSPFDGT-----RVGDVIEADAASLDVAMAAAHRAFSAWGAQPAETRAQILERAAALIES 604

Query: 61   DADNLATMISRETGKPLWEARTEVDSVVNKVEISIRAYADRTSQRKLDSALQGTAA---- 116
                L  ++  E GK L +A  EV    +      R YA+   +   + AL G       
Sbjct: 605  RRGRLIALLQSEGGKTLDDALAEVREAADYC----RYYANVARELMRERALPGPTGEENR 660

Query: 117  LRHKPHGVLAVLGPYNFPAHLPNGHIVPALIAGNAVVFKPSEKTPATGEMLAQCFHRAGI 176
            LRH   GV   + P+NFP  +  G I  AL+AGNAV  KP+E+TP  G         AG+
Sbjct: 661  LRHVGRGVFVCISPWNFPLAIFVGQIAAALVAGNAVAAKPAEQTPLIGFEAVALLREAGV 720

Query: 177  PAAVVQVLIGGPEEGQALVAHDGIDGVLFTGSAHAGIAINRKLASNPGKIVAL--EMGGN 234
            PA  +Q L G    G +LVAH+   GV+FTGS      INR LA  PG IV L  E GG 
Sbjct: 721  PADALQFLPGDGAVGASLVAHELTAGVVFTGSVAVAQEINRALAKKPGPIVPLIAETGGI 780

Query: 235  NPIVVWDTPKIEDAATLIVQSAFTSAGQRCTAARRLIIKASMFDEVIDHVKRLADRIIVG 294
            N ++V  T   E  A  +  SAF SAGQRC+A R L ++  +FD  +  +   A  + +G
Sbjct: 781  NAMIVDSTALFEHVADDVCASAFRSAGQRCSALRLLYLQEEIFDACLATIVGAAKELRLG 840

Query: 295  APFDDPAPFMGPVIDNRTADGLTESFVYLLSSGGRPIKHMVRLQEDRPFLSPAIIDVTAV 354
             P  DPA  +GPVID      L +      + G   + +         F++P ++ +++ 
Sbjct: 841  DP-GDPATHIGPVIDRGAKAALDDYLARRRAEGS--VVYTGAAPGQGCFVAPHVVRLSSG 897

Query: 355  ADRPDVELFGPLLQVV--RVDDFDEAIAEANNTRFGLSASLIGGDPQDYNRFWANIRAGV 412
             +  + E+FGP+L V   R  DFD  +AE     +GL+  L         R  A   AG 
Sbjct: 898  REL-NQEIFGPVLHVAPWRAGDFDSLVAEIMAANYGLTIGLHSRIEARAKRLAALAPAGN 956

Query: 413  VNWNRPTNGA-SSAAPFGGVGLSGNHRPSAYYAADYCAYPVASTEVDQPRASIGVGLR 469
            +  NR   GA   + PFGG  LSG    +    ADY    V    V    A++G  LR
Sbjct: 957  IYINRTMIGAVVGSQPFGGFNLSGTGPKAG--GADYLRRFVREITVTTNTAALGGDLR 1012


Lambda     K      H
   0.319    0.135    0.403 

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: 1125
Number of extensions: 55
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: 471
Length of database: 1018
Length adjustment: 39
Effective length of query: 432
Effective length of database: 979
Effective search space:   422928
Effective search space used:   422928
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 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