GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6938534
          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:

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