GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Pseudomonas fluorescens FW300-N2E3

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 AO353_24475 AO353_24475 aldehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_24475 AO353_24475 aldehyde
           dehydrogenase
          Length = 477

 Score =  520 bits (1339), Expect = e-152
 Identities = 255/471 (54%), Positives = 334/471 (70%)

Query: 11  LLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHER 70
           L I G W +    ++I V+NPAT + IG +A A +AD++ A  AA+ GF  W++V A ER
Sbjct: 6   LFIGGVWRNTHPDESIPVINPATEEQIGLIAKASLADIEDAAIAAEKGFATWKQVSALER 65

Query: 71  AATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVP 130
           A  M KAA+L+RERA+ IA ++T E GKPL EA  EV + AD I+W A+EGRR YGR++P
Sbjct: 66  ATIMHKAASLIRERAENIALILTTEHGKPLGEAMGEVAATADTIDWHAEEGRRAYGRVIP 125

Query: 131 PRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAAL 190
            R LG  Q  V EP+GPV  F PWNFP+ Q V+K++ ALA GCS ++K   E P     L
Sbjct: 126 SRALGVHQFTVMEPIGPVVGFAPWNFPLIQAVKKVAGALAAGCSIILKGATEAPTCAVEL 185

Query: 191 LRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRA 250
           ++AF DAGV  G + L++GD  +IS +LI HP IRKVTFTGSTPVGK+LASLAGLHMKR+
Sbjct: 186 VKAFADAGVSPGAVNLLFGDSGQISEHLIAHPSIRKVTFTGSTPVGKKLASLAGLHMKRS 245

Query: 251 TMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKH 310
           TMELGGHAPVIV +DAD+A AVK +  AK+RNAGQVC+SPTRFLVH+ + DEF    V+ 
Sbjct: 246 TMELGGHAPVIVMDDADIATAVKISVAAKYRNAGQVCVSPTRFLVHSKVFDEFVSRFVEG 305

Query: 311 AEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTV 370
           A  + VG+GL+   T+G +A+  RL A   ++ +A   GA +ETGG RIG +G FF PTV
Sbjct: 306 ARAVMVGDGLDPNVTMGPMAHAGRLKATEELVADAVSHGAKLETGGNRIGHKGYFFEPTV 365

Query: 371 IANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQR 430
           + NVP+ A    +EPFGP+A I  FD ++EAI EANRLP+GL+ YA+TRS ++ + L   
Sbjct: 366 LTNVPVTARAMIDEPFGPIALINSFDDIDEAIKEANRLPYGLSAYAYTRSLSSANKLFNG 425

Query: 431 LEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTVMAV 481
           +E G + IN  +   PE PFGGVKDSGYG+EGGP AL+ ++ TK V++ +V
Sbjct: 426 IESGAISINHHSVALPEHPFGGVKDSGYGTEGGPGALDAFMTTKFVSLASV 476


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: 660
Number of extensions: 22
Number of successful extensions: 1
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: 477
Length adjustment: 34
Effective length of query: 447
Effective length of database: 443
Effective search space:   198021
Effective search space used:   198021
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 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