GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Lentibacillus jeotgali Grbi

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_010531948.1 ON01_RS15275 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_000224785.1:WP_010531948.1
          Length = 488

 Score =  707 bits (1824), Expect = 0.0
 Identities = 337/478 (70%), Positives = 411/478 (85%), Gaps = 2/478 (0%)

Query: 6   KLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAV 65
           +LKNYI G+W+E+K+D+ E V+NPAT EV+ +VPIS+ ED+D+A + A EAF+ W ++AV
Sbjct: 10  QLKNYIGGKWIEAKSDKTESVINPATGEVIAEVPISSNEDVDHAVEVAHEAFQDWKELAV 69

Query: 66  PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGD 125
           P+RARILF +QQLL  H +ELA LITIENGKN KEA GEV RGIENVEFAAGAP+LMMGD
Sbjct: 70  PKRARILFKYQQLLVDHWDELAELITIENGKNLKEAKGEVQRGIENVEFAAGAPNLMMGD 129

Query: 126 SLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLT 185
            L+SIA+ +E+  YRYPIGVVGGI PFNFPMMVPCWMFPMAIA GNTFI+KPSERTPLL 
Sbjct: 130 QLSSIASGLESGVYRYPIGVVGGITPFNFPMMVPCWMFPMAIATGNTFIMKPSERTPLLA 189

Query: 186 EKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLK 245
            +L EL E+AGLP+GVFN+V+GAHDVVNG+L+H ++ AISFVGS+PV E+VYK+G++NLK
Sbjct: 190 NRLAELLEEAGLPEGVFNIVHGAHDVVNGLLDHDKVAAISFVGSQPVAEHVYKRGTDNLK 249

Query: 246 RVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQ 305
           RVQ+L+GAKNHTIVLNDAN+++  T I+ AAFGSAGERCMA +VV VEE +ADEF+ +L 
Sbjct: 250 RVQALSGAKNHTIVLNDANMDNASTQILNAAFGSAGERCMAASVVAVEESVADEFIDQLI 309

Query: 306 EKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRE--NVSDDGYF 363
           +K  +I IGNGLD+ VFLGPVIRE +K+RTL YIE G  EGA+L+ DGRE  N  + GYF
Sbjct: 310 KKANEINIGNGLDEDVFLGPVIREQHKERTLGYIETGENEGAKLIRDGREDGNAQEKGYF 369

Query: 364 VGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIR 423
           VGPTIFDNVTTEM IW++EIFAPVLS++RVK+L EAI++ N+S FANG+CLFT +  ++R
Sbjct: 370 VGPTIFDNVTTEMKIWQEEIFAPVLSIVRVKDLDEAIDVTNQSPFANGSCLFTRDGGSVR 429

Query: 424 YFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTARY 481
            FRENIDAGMLGIN+GVPAPMAFFPFSGWK SF+G LHANGKDSV+FYTRKKV+T R+
Sbjct: 430 QFRENIDAGMLGINIGVPAPMAFFPFSGWKDSFYGDLHANGKDSVEFYTRKKVMTTRW 487


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: 741
Number of extensions: 33
Number of successful extensions: 2
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: 488
Length adjustment: 34
Effective length of query: 453
Effective length of database: 454
Effective search space:   205662
Effective search space used:   205662
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