Aligments for a candidate for gabD in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for gabD in Shewanella oneidensis MR-1

Align succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16 (characterized)
to candidate 201293 SO2136 aldehyde-alcohol dehydrogenase (NCBI ptt file)

Query= CharProtDB::CH_007085
         (453 letters)



>FitnessBrowser__MR1:201293
          Length = 866

 Score =  303 bits (776), Expect = 1e-86
 Identities = 162/439 (36%), Positives = 255/439 (58%), Gaps = 8/439 (1%)

Query: 1   MSNEVSIKELIEKAKVAQKKLEAYSQEQVDVLVKALGKVVYDNAEMFAKEAVEETEMGVY 60
           ++N   +  ++E+   AQ +  ++SQ QVD + +A      D     AK A  ET MGV 
Sbjct: 3   VTNAQKLDLMVERVARAQAEYASFSQAQVDAIFRAAALAAADARISLAKMAAAETRMGVI 62

Query: 61  EDKVAKCHLKSGAIWNHIKDKKTVGIIKEEPERALVYVAKPKGVVAATTPITNPVVTPMC 120
           EDKV K H  S  I+N  KD+KT GI+ E+P    + +A+P G++    P TNP  T + 
Sbjct: 63  EDKVIKNHFASEYIYNKYKDEKTCGILSEDPTFGTITIAEPVGIICGIVPTTNPTSTAIF 122

Query: 121 NAMAAIKGRNTIIVAPHPKAKKVSAHTVELMNAELKKLGAPENIIQIVEAPSREAAKELM 180
            A+ ++K RN II +PHP+AK  +    +L+       GAP++II  ++ PS   + +LM
Sbjct: 123 KALISLKTRNAIIFSPHPRAKVSTTTAAKLVLDAAIAAGAPKDIIGWIDEPSVALSNQLM 182

Query: 181 --ESADVVIATGGAGRVKAAYSSGRPAYGVGPGNSQVIVDKGYDYNKAAQDIITGRKYDN 238
                ++++ATGG G VKAAYSSG+PA GVG GN+ +++D+  D  +A   I+  + +DN
Sbjct: 183 THPKVNLILATGGPGMVKAAYSSGKPAIGVGAGNTPIVIDETADIKRAVSSILMSKTFDN 242

Query: 239 GIICSSEQSVIAPAEDYDKVIAAFVENGAFYVEDEETVEKFRSTLFKDGKINSKIIGKSV 298
           G++C+SEQ+VI     Y++V   F  +G + +   +T E  +  + K+G +N+ I+G+S 
Sbjct: 243 GVVCASEQAVIVVDSIYEQVKERFATHGGYLLNAAQT-EAMQQVILKNGGLNADIVGQSA 301

Query: 299 QIIADLAGVKVPEGTKVIVLKGKGAGEKDVLCKEKMCPVLVALKYDTFEEAVEIAMANYM 358
             IA +AG++VP  TKV++ +     E +    EK+ P+L   +   F +AV+ A     
Sbjct: 302 ATIAQMAGIEVPHTTKVLIGEVTDISETEAFAHEKLSPLLGMYRAADFNDAVDKAETLVA 361

Query: 359 YEGAGHTAGIHSDND---ENIRYAGTVLPISRLVVNQPATTA--GGSFNNGFNPTTTLGC 413
             G GHT+G+++D D   E ++  G  +  +R+++N PA+    G  +N    P+ TLGC
Sbjct: 362 LGGIGHTSGLYTDQDTQTERVKSFGFRMKTARILINTPASQGGIGDLYNFKLAPSLTLGC 421

Query: 414 GSWGRNSISENLTYEHLIN 432
           GSWG NSISEN+   HLIN
Sbjct: 422 GSWGGNSISENVGPSHLIN 440


Lambda     K      H
   0.313    0.131    0.368 

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: 873
Number of extensions: 45
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 453
Length of database: 866
Length adjustment: 37
Effective length of query: 416
Effective length of database: 829
Effective search space:   344864
Effective search space used:   344864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources