GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Shewanella sp. ANA-3

Align succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16 (characterized)
to candidate 7024610 Shewana3_1788 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)

Query= CharProtDB::CH_007085
         (453 letters)



>FitnessBrowser__ANA3:7024610
          Length = 866

 Score =  299 bits (765), Expect = 3e-85
 Identities = 161/439 (36%), Positives = 253/439 (57%), Gaps = 8/439 (1%)

Query: 1   MSNEVSIKELIEKAKVAQKKLEAYSQEQVDVLVKALGKVVYDNAEMFAKEAVEETEMGVY 60
           ++N   +  ++E+   AQ +  ++SQ QVD + +A      D     AK A  ET MGV 
Sbjct: 3   VTNAQELDLMVERVAKAQAEYASFSQAQVDAIFRAAALAAADARISLAKMAAAETRMGVI 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    +  + K+G +N+ I+G+S 
Sbjct: 243 GVVCASEQAVIVVDSIYEQVKERFATHGGYLLNAAQTA-AMQQVILKNGGLNADIVGQSA 301

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

Query: 359 YEGAGHTAGIHSDND---ENIRYAGTVLPISRLVVNQPATTA--GGSFNNGFNPTTTLGC 413
             G GHT+G+++D D   E ++  G  +  +R+++N PA+    G  +N    P+ TLGC
Sbjct: 362 LGGIGHTSGLYTDQDTQTERVKTFGFRMKTARILINTPASQGGIGDLYNFKLAPSLTLGC 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: 867
Number of extensions: 42
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:

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