GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Methylocella silvestris BL2

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_012591341.1 MSIL_RS11965 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-16244
         (495 letters)



>NCBI__GCF_000021745.1:WP_012591341.1
          Length = 506

 Score =  341 bits (874), Expect = 4e-98
 Identities = 197/485 (40%), Positives = 276/485 (56%), Gaps = 21/485 (4%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           FI  ++      ++F  +SP     +  +  + +ED++ A++AA AA   SW  + P  R
Sbjct: 22  FIGGKWTPPVKGQSFENISPIDGNVVCTIARSTAEDVELALDAAHAA-RESWGNASPATR 80

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSVI 142
             VL ++AD I+E  D LA +E +DNGK +  +K  D+ L   +FR  AG     +GS+ 
Sbjct: 81  SLVLLRIADRIEEKLDVLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGVLRAQEGSIS 140

Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
           E       Y   EP+GV  QIIPWNFPLLMA WK+ P L  G   V+K AE TP+S + L
Sbjct: 141 EIDHDTIAYHFHEPLGVVAQIIPWNFPLLMAVWKIAPALAAGNCIVMKPAEQTPMSIMVL 200

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
             +I +   PPGV+NV++GFG   G P++  P+I KVAFTG T TGR IM+ A+E N+  
Sbjct: 201 MDVIGDL-LPPGVLNVINGFGVECGKPLAQSPRIAKVAFTGETTTGRLIMQYASE-NIIP 258

Query: 263 VTLELGGKSPNIVFDDA-----DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317
           VTLELGGKSPNI F+D      D              N GEVC   SR  V E IYD+ +
Sbjct: 259 VTLELGGKSPNIFFEDVADEDDDYFDKALEGFAMFALNQGEVCTCPSRALVHEKIYDRFM 318

Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG---- 373
                   ++K G+P    T +GAQ S  QL+KIL Y+DIG++EGA V+ GG R      
Sbjct: 319 ERAIKRVNAIKQGNPLDPSTMIGAQASNDQLEKILSYMDIGRQEGAKVLAGGGRADLGPE 378

Query: 374 -NKGYFIKPTIFGDVKEDH---QIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGV 429
              G++++PT+     E H   +I ++EIFGPV+++T FK   + + +AND+ YGL +GV
Sbjct: 379 LANGFYVQPTVL----EGHNKMRIFQEEIFGPVLSVTTFKDDAQALEIANDTLYGLGSGV 434

Query: 430 HTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489
            T N + A      I +G +W N Y+ +     FGGY +SGIGRE  +  LD+Y Q K +
Sbjct: 435 WTRNGTRAYRFGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGIGRENHKMMLDHYQQTKNM 494

Query: 490 RIGLS 494
            +  S
Sbjct: 495 LVSYS 499


Lambda     K      H
   0.316    0.133    0.389 

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: 596
Number of extensions: 26
Number of successful extensions: 7
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: 495
Length of database: 506
Length adjustment: 34
Effective length of query: 461
Effective length of database: 472
Effective search space:   217592
Effective search space used:   217592
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: 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