GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Brucella inopinata BO1

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_008506742.1 BIBO1_RS10835 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-11560
         (497 letters)



>NCBI__GCF_000182725.1:WP_008506742.1
          Length = 505

 Score =  370 bits (951), Expect = e-107
 Identities = 205/476 (43%), Positives = 288/476 (60%), Gaps = 12/476 (2%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           FI G++ +  SG  FE  SPV+G+ L +VA  D AD   A++ A A     +W + + A+
Sbjct: 21  FIGGKWVEPRSGRYFENTSPVNGQVLCEVARSDAADVEAALDAAHAA--KELWGRTSVAE 78

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R   L R AD + +N+  LA  ET D GKPI ++++ D+P A     + A  I      +
Sbjct: 79  RALILNRIADRIEENLPALAAAETWDNGKPIRETTNADLPLAVDHFRYFAGVIRAQEGGI 138

Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
           +   HD +     EP+GVVG I+PWNFPLLMA WKL PALA GN VVLKP+E++P + + 
Sbjct: 139 SEIDHDTVAYHFHEPLGVVGQIIPWNFPLLMATWKLAPALAAGNCVVLKPAEQTPASILV 198

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
           + +L  +  +P GV+N++ G+G   GK LA    +  + FTG T   + +M YA + N+ 
Sbjct: 199 LMELIADI-LPPGVVNIVNGFGLEAGKPLASSPRIAKIAFTGETTTGRLIMQYASQ-NLI 256

Query: 263 RIWLEAGGKSPNIVFADA----PDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318
            + LE GGKSPNI F D      D    A       A NQGEVCT  SR L++ SI D+F
Sbjct: 257 PVTLELGGKSPNIFFKDVAAEDDDFLDKAIEGFVMFALNQGEVCTCPSRALIQESIYDRF 316

Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL--- 375
           +   ++ ++    G+PLDP T +GA   ++Q+  +LSY++ G ++GA++LAGG+R +   
Sbjct: 317 MEKALKRVEAIVQGDPLDPATMIGAQASSEQLEKILSYLDIGRQEGAEVLAGGERNMLPG 376

Query: 376 EETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435
           +  GG YV+PT+F G  N MRI QEEIFGPV+SV  F    EA++IANDT YGL AGIWT
Sbjct: 377 DLAGGYYVKPTVFKG-HNKMRIFQEEIFGPVVSVATFKDDAEALSIANDTLYGLGAGIWT 435

Query: 436 SDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
            D ++A++  RA++AG VW N Y      A FGG+KQSG GR+  L  L+ Y   K
Sbjct: 436 RDGTRAYRFGRAIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHLKMLDHYQNTK 491


Lambda     K      H
   0.316    0.132    0.390 

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: 630
Number of extensions: 32
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: 497
Length of database: 505
Length adjustment: 34
Effective length of query: 463
Effective length of database: 471
Effective search space:   218073
Effective search space used:   218073
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 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