GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Salinicoccus carnicancri Crm

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate WP_017547432.1 C792_RS0100265 L-glutamate gamma-semialdehyde dehydrogenase

Query= reanno::Caulo:CCNA_01360
         (500 letters)



>NCBI__GCF_000330705.1:WP_017547432.1
          Length = 514

 Score =  178 bits (451), Expect = 5e-49
 Identities = 135/462 (29%), Positives = 217/462 (46%), Gaps = 18/462 (3%)

Query: 6   PHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQR 65
           P  IGG+ ++    +       +  +    V+ A+ G ++ A   A  A   W+  +P+ 
Sbjct: 38  PLIIGGEHIE-TDDQITSYNPSDKEQAVGHVSKATQGHIDAAFQAAGEAFETWSEWDPKD 96

Query: 66  RARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEF-ACGVPHLLKGEY 124
           RA ++     ++     E +AL+  E GK   ++ GD   G++ IE+ A  +  L  G+ 
Sbjct: 97  RAELLIRVAAIIRRRKHEFSALMVHEAGKPWNEADGDTNEGIDFIEYYARSMMELADGKP 156

Query: 125 TQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPV 184
                   + Y   QP+G    I+P+NFP  I        I  GN  +LKP+E  P +  
Sbjct: 157 VLDREGEHNKY-FYQPMGTGVTISPWNFPFAIMTGTTVAPIIAGNTVLLKPAEDTPLISY 215

Query: 185 RLAELMIEAGLPPGVLNVVHGDKDCV-EAILDHPDIKAVSFVGSSDIAQSVFQRAGAAG- 242
           +L E+  EAGLP GV+N V GD   + + ++DH     ++F GS      + +RA     
Sbjct: 216 KLMEVFEEAGLPKGVVNFVTGDPGVIGDYMVDHHKTHFITFTGSKSTGLRISERASVVQE 275

Query: 243 -----KRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTAT 297
                KRV    G K+  +V   ADLD A   I+ +A+G AG++C A    V + E    
Sbjct: 276 GQHFLKRVITEMGGKDTIIVDKTADLDLAADSIVSSAFGFAGQKCSAGSRAV-IHEDVYD 334

Query: 298 ALREKLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSL 357
            + +K V     L VG   D + + GPV+S      I+ YI +G  EG  L + G     
Sbjct: 335 EVLKKAVELTEELTVGNPVD-ETYMGPVISRKQFDMIKGYIDIGKGEGT-LKIGGE---- 388

Query: 358 QGHEEGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIF 417
               +G+F+ PT+F  + P +R   +EIFGPV+   +A+  +E + +A+   YG   ++ 
Sbjct: 389 TDDSKGYFIQPTIFADLDPKARIMQEEIFGPVVAFAKAKDFDELLEIANNTVYGLTGSVI 448

Query: 418 TRNGDAAREFADQVEVGMVGINVPIPVPV-AYHSFGGWKRSG 458
           T   +   +   +  VG + +N      V  YH FGG+K SG
Sbjct: 449 TNTRENWIKAQKKFHVGNLYLNRGCTAAVMGYHPFGGFKLSG 490


Lambda     K      H
   0.320    0.137    0.409 

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: 611
Number of extensions: 36
Number of successful extensions: 6
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: 500
Length of database: 514
Length adjustment: 34
Effective length of query: 466
Effective length of database: 480
Effective search space:   223680
Effective search space used:   223680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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