GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Marinobacter adhaerens HP15

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF4092 HP15_4032 betaine aldehyde dehydrogenase

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



>FitnessBrowser__Marino:GFF4092
          Length = 486

 Score =  341 bits (875), Expect = 3e-98
 Identities = 196/483 (40%), Positives = 276/483 (57%), Gaps = 11/483 (2%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           +ING+Y  + SG  F+ ++P +G+ ++KV      + + AV+ ARA    G W ++   +
Sbjct: 7   YINGQYVGSASGRLFDNVNPANGKVISKVHEAGREEVDAAVKAARAALR-GPWGKMTLEQ 65

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R A L + AD +    +E    E LD GKP   +S IDIP  A      A+ I  V  E 
Sbjct: 66  RTAILHKVADGINARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADMIKNVPTES 125

Query: 143 --APTPHDQ--LGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPL 198
              PTP     L    R P GV+G I PWN PLL+  WK+GPALA GN+VV+KPSE++P 
Sbjct: 126 FEMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPT 185

Query: 199 TAIRIAQLAIEAGIPAGVLNVLPGYG-HTVGKALALHMDVDTLVFTGSTKIAKQLMVYAG 257
           T   + ++  EAG+P GV NV+ G+G  + G  L  H  VD   FTG T   + +M  A 
Sbjct: 186 TTALLGEVMKEAGVPDGVYNVVHGFGGDSAGAYLTEHPQVDGFTFTGETGTGEVIMKAAA 245

Query: 258 ESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317
           +  ++ I LE GGK+  +VFAD  D++ A E    +   N G+VC    R+ VERSI D+
Sbjct: 246 KG-IRDISLELGGKNAGLVFADC-DMEKAIEGTMRSAFANCGQVCLGTERVYVERSIFDE 303

Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGG---KRT 374
           F+  + EA +G K G P D    +G LV  +    VLSY +    DGA ++ GG      
Sbjct: 304 FVGRLKEAAEGLKIGPPDDADANLGPLVSLKHREKVLSYYQKAVDDGATVVTGGGVPDMP 363

Query: 375 LEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIW 434
            E  GG +VEPTI+ G+ +   +  +EIFGP   +  FDT EEA+ +AN  PYGLA+ IW
Sbjct: 364 AELAGGAWVEPTIWTGLPDDSAVVTDEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIW 423

Query: 435 TSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATW 494
           + +I++AH+ A  + AG +WVN +   D+  PFGG KQSG GR+  +H+LE YTE+K   
Sbjct: 424 SENITRAHRVAGQIEAGIIWVNSWFLRDLRTPFGGSKQSGVGREGGVHSLEFYTEMKNIC 483

Query: 495 IKL 497
           +KL
Sbjct: 484 VKL 486


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: 649
Number of extensions: 38
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: 497
Length of database: 486
Length adjustment: 34
Effective length of query: 463
Effective length of database: 452
Effective search space:   209276
Effective search space used:   209276
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 17 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