GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Methylocystis bryophila S285

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein

Query= SwissProt::O50174
         (487 letters)



>NCBI__GCF_002117405.1:WP_085772038.1
          Length = 506

 Score =  170 bits (430), Expect = 1e-46
 Identities = 148/469 (31%), Positives = 224/469 (47%), Gaps = 26/469 (5%)

Query: 4   HYIAGQWLAGQG-ETLESLDPV-GQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQ 61
           ++I GQW+A  G E  +++ P+ G  +    RG  A  V+ A+ AA +A  AW + P  +
Sbjct: 21  NFIGGQWVAPLGGEYFDNISPITGHPICQVARGR-AADVELALDAAHKAKDAWGKTPAAE 79

Query: 62  RIELLERFAATLKSRADELARVIGEETGKPLWES-ATEVTSMVNKVAISVQAFRERTGEK 120
           R  +L + A  L      LA V   + GKP+ E+ A ++   ++         R + G  
Sbjct: 80  RANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQEGSL 139

Query: 121 SGPLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAEL 180
           S    D  A   H+P GVV    P+NFP  +    + PAL AGNCVV KP+E TP ++ L
Sbjct: 140 SEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQTP-MSIL 198

Query: 181 TLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQK 239
            +   I   LP GVLN+V G G E G  LA+++ +  + FTG + TG L+  Q+  +   
Sbjct: 199 AVAELIADLLPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLI-MQYAAENLI 257

Query: 240 ILALEMGGNNP------LVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGD 293
            + LE+GG +P      ++ E+ A LD A+      A ++ G+ CTC  R LV +  + D
Sbjct: 258 PVTLELGGKSPNIFFADVMAEDDAFLDKALEGFASFA-LNQGEVCTCPSRALVQRSIY-D 315

Query: 294 ALLARLVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPI 353
             + + +A  A +R G     PA  +GA  S    E +L   +    +GA+ L+   + +
Sbjct: 316 KFMEKALARVAKIRQGH-PLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIGGERSV 374

Query: 354 DGAAL-----LTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGL 408
               L     + P  L+         EE FGP++ V  +     A++ AN T YGL AGL
Sbjct: 375 LEGELKEGYYMQPTALEGHNRMRVFQEEIFGPVVSVTTFETEEEALQIANDTLYGLGAGL 434

Query: 409 LSDSRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASG----NHR 453
            +    R  +     RAG V W        + A FGG   SG    NH+
Sbjct: 435 WTRDGSRAYRCGRAIRAGRV-WTNCYHAYPAHAAFGGYKQSGIGRENHK 482


Lambda     K      H
   0.318    0.134    0.396 

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: 543
Number of extensions: 31
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: 487
Length of database: 506
Length adjustment: 34
Effective length of query: 453
Effective length of database: 472
Effective search space:   213816
Effective search space used:   213816
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: 52 (24.6 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