GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Rhodobacter viridis JA737

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_110805439.1 C8J30_RS08590 betaine-aldehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_003217355.1:WP_110805439.1
          Length = 483

 Score =  243 bits (621), Expect = 8e-69
 Identities = 157/470 (33%), Positives = 238/470 (50%), Gaps = 7/470 (1%)

Query: 9   NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68
           +++NG WVE       +V+ P T EV+  +  +T   I+ A   A  A + W+ +    R
Sbjct: 9   HFVNGNWVEDAAGAEIEVIFPGTGEVIAILHEATPAVIEEALAGAQAAQRAWAALKPVER 68

Query: 69  ARILFNFQQLLSQHKEELAHLITIENGKNTKE-ALGEVGRGIENVEFAAGAPSLMMGDSL 127
           ARIL     L+   + ELA L T++ GK  +E ++ +   G +++E+ AG    + G+++
Sbjct: 69  ARILRRAADLIRARRAELALLETLDTGKPIQETSVADWPSGADSLEYFAGLAPTLTGETI 128

Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187
             +  D  A   R P+GV  GI  +N+P  + CW    A++ GN  I KPSE TPL   +
Sbjct: 129 P-LGGDF-AYTIREPLGVCVGIGAWNYPSQIACWKAAPALSTGNAMIFKPSEITPLGALQ 186

Query: 188 LVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRV 247
           L  +F +AG+P GVFNVV G   V   +     +  +S  GS P G  VY      +K V
Sbjct: 187 LAAIFVEAGMPAGVFNVVQGRGAVGGRLATDSRVAKVSLTGSVPTGAKVYAAAGAGMKHV 246

Query: 248 QSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEK 307
               G K+  IV  DA+LE  +   +   F S+G+ C     V V + I + F+ +L E+
Sbjct: 247 TMELGGKSPLIVFEDADLESAIGAAMLGNFYSSGQICSNGTRVFVHKAIKERFLTRLAER 306

Query: 308 VADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPT 367
            A IK G+ LD+    GP++      + L YI     EGARLVC G    ++   FV PT
Sbjct: 307 TAAIKAGDPLDETTQFGPLVSAAQHAKVLGYIATAKSEGARLVCGGAAG-AEGALFVQPT 365

Query: 368 IFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFRE 427
           +F +VT  MTI ++E+F PV++V+  +   E I  AN ++F   A +FT++         
Sbjct: 366 VFADVTDSMTIAREEVFGPVMAVLDFETEDEVIARANGTDFGLAAGVFTADLARGHRVIA 425

Query: 428 NIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477
            + AG   IN     P+   PF   KSS  G    N K +++ YT+ K V
Sbjct: 426 QLQAGTTWINAYNLTPVE-MPFGAVKSS--GVGRENSKAAIEHYTQVKAV 472


Lambda     K      H
   0.318    0.136    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: 527
Number of extensions: 27
Number of successful extensions: 3
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: 483
Length adjustment: 34
Effective length of query: 453
Effective length of database: 449
Effective search space:   203397
Effective search space used:   203397
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 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