GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Shewanella sp. ANA-3

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 7025959 Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)

Query= BRENDA::P05091
         (517 letters)



>lcl|FitnessBrowser__ANA3:7025959 Shewana3_3107
           methylmalonate-semialdehyde dehydrogenase [acylating]
           (RefSeq)
          Length = 496

 Score =  218 bits (554), Expect = 5e-61
 Identities = 152/482 (31%), Positives = 246/482 (51%), Gaps = 15/482 (3%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           ++N E H A S ++     P+TGE   QV+   +++V  A+  A++AF     W ++   
Sbjct: 7   YVNGE-HTAASTRSQEIFEPATGECRGQVSLASRDEVSAAIAIAKSAFDT---WSQVTPL 62

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
           +R R+L +   L+E+    LA L TL++GK  +     +L   L+ + +  G      G+
Sbjct: 63  NRARVLFKFKALVEQHMDELAQLITLEHGK-VLDDARGELIRGLEVVEFACGIPHLLKGE 121

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

Query: 219 LYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSN 278
           + +A L+ +AG P GV N+V G    A   + SHED+  V+F GST I   I   A S +
Sbjct: 182 MRIAELLTQAGLPAGVFNVVNG-DKEAVDTLLSHEDIQAVSFVGSTPIAEYIYSTA-SKH 239

Query: 279 LKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338
            KRV    G K+  ++M DAD+D AV     A + + G+ C A S      D+ D+ V++
Sbjct: 240 GKRVQALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGDVGDKLVDK 299

Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGG--IAAD--R 394
            + + +   VGN    + E GP +      K+  +++ G +EGA L+  G     AD  +
Sbjct: 300 LLPQIQQLKVGNGLTPEMEMGPLISRQHLAKVTEFVDAGVKEGATLVVDGRQLTVADHQQ 359

Query: 395 GYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLD 454
           GYF+   +F +V   M I +EEIFGPV+ I++ K     +   N   +G   A+FT+  +
Sbjct: 360 GYFLGACLFDNVTPEMRIYREEIFGPVLSIVRVKDYASALALINQHEFGNGTAIFTQSGE 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 VP 513
            P
Sbjct: 480 WP 481


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: 569
Number of extensions: 28
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: 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 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