GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacF in Escherichia coli BW25113

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 15646 b1525 putative aldehyde dehydrogenase (VIMSS)

Query= SwissProt::Q1JUP4
         (481 letters)



>lcl|FitnessBrowser__Keio:15646 b1525 putative aldehyde
           dehydrogenase (VIMSS)
          Length = 462

 Score =  270 bits (690), Expect = 8e-77
 Identities = 155/434 (35%), Positives = 229/434 (52%), Gaps = 4/434 (0%)

Query: 29  VNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAATMRKAAALVRERADAI 88
           +NPATG+ +  +  AG  D++ AL  A +GF  WR+     RA  +R     +R R++ +
Sbjct: 12  INPATGEQLSVLPWAGADDIENALQLAAAGFRDWRETNIDYRAEKLRDIGKALRARSEEM 71

Query: 89  AQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPRNLGAQQTVVK-EPVGP 147
           AQ++T+E GKP+ +AR EV  +A++ +W+A+ G  +      P  +  QQ V++  P+G 
Sbjct: 72  AQMITREMGKPINQARAEVAKSANLCDWYAEHGPAMLK--AEPTLVENQQAVIEYRPLGT 129

Query: 148 VAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAFVDAGVPAGVIGLV 207
           + A  PWNFP+ QV+R     +  G  +L+K           + + F DAG+P GV G +
Sbjct: 130 ILAIMPWNFPLWQVMRGAVPIILAGNGYLLKHAPNVMGCAQLIAQVFKDAGIPQGVYGWL 189

Query: 208 YGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATMELGGHAPVIVAEDAD 267
             D   +S  +I    I  VT TGS   G  + + AG  +K+  +ELGG  P IV  DAD
Sbjct: 190 NADNDGVSQ-MIKDSRIAAVTVTGSVRAGAAIGAQAGAALKKCVLELGGSDPFIVLNDAD 248

Query: 268 VALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEGLKVGNGLEEGTTLG 327
           + LAVKAA   +++N GQVC +  RF++   I   FT   V  A  LK+G+  +E   LG
Sbjct: 249 LELAVKAAVAGRYQNTGQVCAAAKRFIIEEGIASAFTERFVAAAAALKMGDPRDEENALG 308

Query: 328 ALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIANVPLDADVFNNEPFG 387
            +A       +   ++     GA +  GGE++   GN++ PTV+ANV  +   F  E FG
Sbjct: 309 PMARFDLRDELHHQVEKTLAQGARLLLGGEKMAGAGNYYPPTVLANVTPEMTAFREEMFG 368

Query: 388 PVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEVGMLWINQPATPWPE 447
           PVAAI      E A+  AN   FGL+   FT        +  RLE G ++IN        
Sbjct: 369 PVAAITIAKDAEHALELANDSEFGLSATIFTTDETQARQMAARLECGGVFINGYCASDAR 428

Query: 448 MPFGGVKDSGYGSE 461
           + FGGVK SG+G E
Sbjct: 429 VAFGGVKKSGFGRE 442


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: 485
Number of extensions: 22
Number of successful extensions: 3
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: 462
Length adjustment: 33
Effective length of query: 448
Effective length of database: 429
Effective search space:   192192
Effective search space used:   192192
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