GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Shewanella amazonensis SB2B

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)

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



>lcl|FitnessBrowser__SB2B:6938534 Sama_2637 succinate-semialdehyde
           dehydrogenase (NAD(P)(+)) (RefSeq)
          Length = 480

 Score =  298 bits (764), Expect = 2e-85
 Identities = 176/475 (37%), Positives = 264/475 (55%), Gaps = 10/475 (2%)

Query: 18  IEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQ 77
           ++ + +INGE+ DA+SGET    +P     +A V      +   A+  A A   +  W  
Sbjct: 9   LKTKCYINGEWRDALSGETVTIANPATNEAIASVPVMGRDETREAIAAAEAALPA--WRA 66

Query: 78  LAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDK 137
           L   +R AKL R+ +L+ +N ++LAL+ T + GKP+ ++   ++  AA  I W AE   +
Sbjct: 67  LTAKERGAKLRRWYELMLENADDLALMMTTEQGKPLAEAKG-EVVYAASFIEWFAEEAKR 125

Query: 138 VYDEVAPTPH-DQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKS 196
           +Y +  P    D+  +V ++ VGV  AI PWNFP  M   K GPALA G ++++KP+ ++
Sbjct: 126 LYGDTIPGHQGDKRIMVIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKPAPQT 185

Query: 197 PLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYA 256
           P TA+ +A+LA EAGIP GV +V+ G    +G  L  +  V  L FTGST +  +LM   
Sbjct: 186 PFTALALAELAAEAGIPPGVFSVVTGDAVAIGNELCENPVVRKLSFTGSTGVGIKLMQQC 245

Query: 257 GESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKD 316
             + +K++ LE GG +P IVF DA DL AA E A  +   N G+ C   +RL V+  + D
Sbjct: 246 APT-LKKVSLELGGNAPFIVFNDA-DLDAAVEGAMISKYRNAGQTCVCANRLYVQDGVYD 303

Query: 317 KFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLE 376
            F   +  A+   K GN  +P  T G L++   +  V S+++     GA L+AGGK    
Sbjct: 304 AFAQKLAAAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGK---- 359

Query: 377 ETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTS 436
             GG ++EP I   V  +M++A+EE FGP+  +  F   ++ +  ANDT +GLAA  +  
Sbjct: 360 PLGGNFMEPAIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGR 419

Query: 437 DISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
           DIS   K A A+  G V VN        APFGG K SG GR+ S + +++Y E+K
Sbjct: 420 DISLIWKVAEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIDEYVEIK 474


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: 568
Number of extensions: 26
Number of successful extensions: 5
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: 480
Length adjustment: 34
Effective length of query: 463
Effective length of database: 446
Effective search space:   206498
Effective search space used:   206498
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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