GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Shewanella loihica PV-4

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 5208453 Shew_0965 methylmalonate-semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__PV4:5208453
          Length = 496

 Score =  222 bits (566), Expect = 2e-62
 Identities = 153/483 (31%), Positives = 244/483 (50%), Gaps = 15/483 (3%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           +IN + H   S ++     P+TGE    V+     +VD A++ A+ A     PW  M   
Sbjct: 7   YINGQ-HTQPSARSAAVFEPATGEHKANVSLASALEVDAAIELAKKAH---GPWSEMTPL 62

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
           +R R+L +   L+E +   LAA+ T ++GK  +     ++   L+ + +  G      G+
Sbjct: 63  NRARILFKFKALVEANMDELAAMITREHGK-VLDDAKGEIIRGLEVVEFACGIPHLLKGE 121

Query: 160 -TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTA 218
            T  + G   ++T ++ +GV   I P+NFP+++  W    A+A GN  +MK +E+ P + 
Sbjct: 122 HTEQVGGGVDAWTLNQSLGVVAGIAPFNFPVMVPMWMFPIAIAAGNTFIMKPSEKDPTSV 181

Query: 219 LYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSN 278
           + +A L+ EAG P GV N+V G    A   + +H+D+  V+F GST I   I   A +  
Sbjct: 182 MRMAELLTEAGLPDGVFNVVNG-DKEAVDTLLTHKDIQAVSFVGSTPIAEYIYQTAAAHG 240

Query: 279 LKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338
            KRV    G K+  ++M DAD+D AV     A + + G+ C A S      ++ D  VE+
Sbjct: 241 -KRVQALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGEVGDALVEK 299

Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAA----DR 394
            + + ++  VGN  + + E GP +      K+  Y++TG  EGA LL  G        ++
Sbjct: 300 LLPQIQALKVGNGLEGEMEMGPLISAQHLDKVRSYVDTGVSEGASLLADGRQLTVADHEQ 359

Query: 395 GYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLD 454
           GYF+   +F  V   MTI KEEIFGPV+ I++ K   E +   N   +G   A+FT+  +
Sbjct: 360 GYFLGGCLFDHVTPEMTIYKEEIFGPVLTIVRVKDYAEALTLINEHEFGNGTAIFTQSGE 419

Query: 455 KANYLSQALQAGTVWVNC-YDVFGAQSPFGGYKMS--GSGRELGEYGLQAYTEVKTVTVK 511
            A +    +Q G V VN    V  A   FGG+K S  G     G  G++ YT+ K +T +
Sbjct: 420 AARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAITAR 479

Query: 512 VPQ 514
            P+
Sbjct: 480 WPK 482


Lambda     K      H
   0.319    0.136    0.409 

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: 585
Number of extensions: 27
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: 517
Length of database: 496
Length adjustment: 34
Effective length of query: 483
Effective length of database: 462
Effective search space:   223146
Effective search space used:   223146
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