GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Shewanella amazonensis SB2B

Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)

Query= metacyc::MONOMER-15732
         (497 letters)



>FitnessBrowser__SB2B:6938534
          Length = 480

 Score =  311 bits (796), Expect = 4e-89
 Identities = 179/480 (37%), Positives = 262/480 (54%), Gaps = 9/480 (1%)

Query: 18  KLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSRL 77
           K K  I  +W+DA SG T++  NPAT E +  VP    ++   A+ AA  A     W  L
Sbjct: 10  KTKCYINGEWRDALSGETVTIANPATNEAIASVPVMGRDETREAIAAAEAALP--AWRAL 67

Query: 78  RPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKI 137
             +ER   L R  +LM  +A  LA +     GK  A A+  +V  A  F+ + A  A ++
Sbjct: 68  TAKERGAKLRRWYELMLENADDLALMMTTEQGKPLAEAKG-EVVYAASFIEWFAEEAKRL 126

Query: 138 EGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVLKP 197
            G T+    P    D+    V ++ +GV  AI  WNFP  +   K GPALA GCT+++KP
Sbjct: 127 YGDTI----PGHQGDK-RIMVIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKP 181

Query: 198 ADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKLI 257
           A +TP + L LAEL  EAG P GVF+VVTG  +  G  L  +P V KL+FTGST VG  +
Sbjct: 182 APQTPFTALALAELAAEAGIPPGVFSVVTGDAVAIGNELCENPVVRKLSFTGSTGVGIKL 241

Query: 258 GKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRKH 317
            +     + +V+LELGG +P IV  DA+L  A  GA  + + N GQ C   +RLYV    
Sbjct: 242 MQQCAPTLKKVSLELGGNAPFIVFNDADLDAAVEGAMISKYRNAGQTCVCANRLYVQDGV 301

Query: 318 FDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGGEGF 377
           +D     +A     +K+GNG +P V  GPLI+A   ++V  +++   + GAT+  GG+  
Sbjct: 302 YDAFAQKLAAAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGKPL 361

Query: 378 GPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLGASIWSND 437
           G G F++P ++ +VD   ++ +EE FGP+     F D+D+VI  AND  +GL A  +  D
Sbjct: 362 G-GNFMEPAIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGRD 420

Query: 438 LAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTELKSVLIKL 497
           ++ + ++   ++ G V VN         PFGG K SG+GRE     I+ Y E+K + + +
Sbjct: 421 ISLIWKVAEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIDEYVEIKYICLSV 480


Lambda     K      H
   0.320    0.137    0.413 

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: 576
Number of extensions: 28
Number of successful extensions: 4
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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