GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Methylocapsa aurea KYG

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate WP_036264374.1 DL86_RS17780 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974
         (488 letters)



>NCBI__GCF_000746085.1:WP_036264374.1
          Length = 1033

 Score =  172 bits (437), Expect = 4e-47
 Identities = 140/456 (30%), Positives = 210/456 (46%), Gaps = 22/456 (4%)

Query: 35   ATAGQVESAVQAARQAFPDWARRTLEERISVLEAFAAALKNHADELAHTIGEETGKPLWE 94
            A  G ++ A++ AR  F  W+R  +  R + L+  A  L+  A    H +  E GK L +
Sbjct: 574  AAPGLLQEAMREARGGFKIWSRTPVGLRAACLDRAAQELEAQAPRWLHLLQIEAGKTLED 633

Query: 95   AATEVTSMVNKIAISVQSYRERTGEKS---GPLGDATAVLRHKPHGVVAVFGPYNFPGHL 151
            A  E    ++      Q  R R    +   GP G+   +  H   GV     P+NFP  +
Sbjct: 634  AIGEWREAIDFCRYYAQEARRRFASPAPMPGPTGEDNRLFCHG-RGVFVCISPWNFPLSI 692

Query: 152  PNGHIVPALLAGNSVLFKPSELTPKVAELTVKCWIEAGLPAGVLNLLQGARETGIALAAN 211
              G I  AL AGNSVL KP+E TP +A   V     AG+PA VL+LL G  + G AL A 
Sbjct: 693  FLGQIAAALAAGNSVLAKPAEQTPLIAAQAVSLLYRAGVPASVLHLLPGDGDVGAALVAL 752

Query: 212  PGIDGLFFTGSSRTGNHLHQQFAGRPDKI--LALEMGGNNPLVVDQVADLDAAVYTIIQS 269
             G+ G+  TGS  T   +++  A +   I  L  E GG N ++ D  A  +     ++ S
Sbjct: 753  DGVAGVAITGSMDTATKINRSLAAKSGPIAQLIAETGGVNAMIADATALPEQVCDDVVAS 812

Query: 270  AFISAGQRCTCARRLLVPQGAWGDSLLARLVAVSSTLSVGAFDQQPAPFMGSVVSLGAAK 329
            AF SAGQRC+ A RLL  Q    D ++A +   +  L VG   +     +G V+ L A +
Sbjct: 813  AFRSAGQRCS-ALRLLCLQEDVADRMIAMIKGAARELLVGD-PRALGVHVGPVIDLAAKR 870

Query: 330  ALMDAQEHLLANGAVALLEMTQPQAQSA-----LLTPGILDVSAVADRPDEELFGPLLQV 384
            +L   + H+    A A++        +A      L P I ++S+V+D    E FGP+L V
Sbjct: 871  SL---EAHIEDMRACAIVHYAGRAPSTAPPRGFYLAPHIFELSSVSDL-RREAFGPILHV 926

Query: 385  IRY--ADFEAAIAEANDTAYGLAAGLLSDSEARYQQFWLESRAGIVNWNKQLTGA-ASSA 441
             RY  ++    +       +GL  G+ S  +A   +      AG    N+ + GA   + 
Sbjct: 927  ARYKASELGGLLDSIEAAGFGLTLGVHSRIDAVIDEIVERRLAGNCYVNRNMIGAVVGTQ 986

Query: 442  PFGGVGASGN--HRASAYYAADYCAYPVASLETPSL 475
            PFGG G SG        +Y   +C     ++ T ++
Sbjct: 987  PFGGFGLSGTGPKAGGPHYLDRFCVEQTVTINTAAV 1022


Lambda     K      H
   0.316    0.132    0.388 

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: 1082
Number of extensions: 57
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: 488
Length of database: 1033
Length adjustment: 39
Effective length of query: 449
Effective length of database: 994
Effective search space:   446306
Effective search space used:   446306
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 (21.6 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. 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