GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacF in Desulfovibrio vulgaris Hildenborough

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein

Query= SwissProt::Q1JUP4
         (481 letters)



>lcl|MicrobesOnline__882:208821 DVU3294 aldehyde dehydrogenase
           (NADP) family protein
          Length = 464

 Score =  193 bits (490), Expect = 1e-53
 Identities = 151/465 (32%), Positives = 220/465 (47%), Gaps = 20/465 (4%)

Query: 25  TIDVVNPATGKPIGRVAHAGIADLDRALAAAQS--GFEAWRKVPAHERAATMRKAAALVR 82
           +I V NP     +G V     A+   AL  A +  G  A R +PAHER A + + A L+R
Sbjct: 3   SITVRNPFDLSTVGEVPLMSEAEAFAALERAHALHGDPAHR-IPAHERLAILERLATLMR 61

Query: 83  ERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVP----PRNLGAQQ 138
             A+A+ +   +E GKP  ++ VEV  A D + W A E  ++ GR VP    P + G   
Sbjct: 62  THAEALVRDAVREGGKPWADSVVEVERAIDGVRWAARELAQLGGREVPMGLTPASAGRLA 121

Query: 139 TVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAFVDAG 198
             V+EP G V A + +N PVN +V +   A A GC  LVK    TP S   +LR   +AG
Sbjct: 122 FTVREPRGVVLAISAFNHPVNLIVHQAVPAFAAGCPVLVKPASATPLSCRNVLRLMHEAG 181

Query: 199 VPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATMELGGHA 258
           VP     ++    A  +  L+  P +  ++F GS+ VG  L S        A +E GG A
Sbjct: 182 VPEAWATML-PCAAATAEKLVADPRVAFLSFIGSSRVGWHLRSKLAPGATCA-LEHGGAA 239

Query: 259 PVIV--AEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEGLKV 316
           PV++  + D D AL +   GG  F +AGQVC+S  R    +     F   L   A  L  
Sbjct: 240 PVVLDASADLDAALPLLLKGG--FYHAGQVCVSVQRVFAPHETARTFAERLAAAAAQLPT 297

Query: 317 GNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIANVPL 376
           G+ +   T +G L +PR ++ +   ++ AR  G ++  GG  +      ++PTV+ + P 
Sbjct: 298 GDPMRHDTAVGPLIDPREVSRVHEWVEEARAGGGTVLCGGAPLSE--TLYSPTVVYDPPQ 355

Query: 377 DADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEVGML 436
              +  NE FGPV A+      +EAIA AN +PF      F R         +RL    +
Sbjct: 356 GCRLARNEVFGPVVAVFSTRDRDEAIARANDVPFIFQAAVFARDVDVALDTARRLNATGV 415

Query: 437 WINQPA---TPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478
            +N        W  MPFGG  +SG G+ G   A+      K + +
Sbjct: 416 MVNDHTAFRVDW--MPFGGRGESGMGTGGIGPAMHEMTTEKLIVL 458


Lambda     K      H
   0.318    0.134    0.393 

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: 32
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: 481
Length of database: 464
Length adjustment: 33
Effective length of query: 448
Effective length of database: 431
Effective search space:   193088
Effective search space used:   193088
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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 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