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_008507152.1 BIBO1_RS11605 NAD-dependent succinate-semialdehyde dehydrogenase

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



>NCBI__GCF_000182725.1:WP_008507152.1
          Length = 483

 Score =  319 bits (818), Expect = 1e-91
 Identities = 185/475 (38%), Positives = 274/475 (57%), Gaps = 10/475 (2%)

Query: 18  IEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQ 77
           ++ +  +NG + DA  G T +  +P DG  +  V S  +A    A++ A A   SG W+ 
Sbjct: 10  LKSQCLVNGRWIDAADGTTIKVTNPADGSVIGTVPSLSVATIKEAID-ASAKALSG-WAA 67

Query: 78  LAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDK 137
               +R   L ++ DL+  N +++AL+ T + GKP+ ++   ++  AA  I W AE   +
Sbjct: 68  KTAKERAGILRKWFDLIIANADDIALIMTSEQGKPLAEARG-EVLYAASFIEWFAEEAKR 126

Query: 138 VYDEVAPTPHDQLGL-VTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKS 196
           VY +  P P +   L V R+PVGV  AI PWNFP  M   K  PALA G +++++P++ +
Sbjct: 127 VYGDTIPAPQNGQRLTVIRQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMIVRPADLT 186

Query: 197 PLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYA 256
           PLTA+ +  LA +AGIPAGVL ++ G    +G  L  +  V  L FTGST++ + LM   
Sbjct: 187 PLTALALGVLAEKAGIPAGVLQIVTGKAREIGAELTSNDTVRKLSFTGSTEVGRLLMAQC 246

Query: 257 GESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKD 316
             + +KRI LE GG +P IVF DA DL AA + A  +   N G+ C   +R+ V+R + D
Sbjct: 247 APT-IKRISLELGGNAPFIVFDDA-DLDAAVDGAMVSKYRNAGQTCVCANRIYVQRGVYD 304

Query: 317 KFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLE 376
           KF   +   +K  K GN  +P   +G +++ + +  V ++IE     GAKL+AGGK    
Sbjct: 305 KFAEKLAAKVKELKVGNGTEPGVVIGPMIEEKAITKVKAHIEDAVSKGAKLIAGGK---- 360

Query: 377 ETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTS 436
           E GG + EP I  GVT+ M +A+EE FGP+  + AFDT EE +A ANDT +GLAA  +T 
Sbjct: 361 ELGGLFFEPGILTGVTSDMLVAKEETFGPLAPLFAFDTEEEVIAQANDTIFGLAAYFYTE 420

Query: 437 DISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
           + S+A + + A+  G V  N     +  APFGG KQSG GR+ S + +E+Y E K
Sbjct: 421 NFSRAIRVSEALEYGMVGHNTGLISNEVAPFGGVKQSGLGREGSKYGIEEYLETK 475


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: 573
Number of extensions: 39
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: 483
Length adjustment: 34
Effective length of query: 463
Effective length of database: 449
Effective search space:   207887
Effective search space used:   207887
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