Align Probable glycerol-3-phosphate dehydrogenase; GPDH; EC 1.1.5.3 (characterized)
to candidate Ac3H11_797 Glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
Query= SwissProt::Q8SR40 (614 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_797 Length = 530 Score = 311 bits (798), Expect = 3e-89 Identities = 189/530 (35%), Positives = 286/530 (53%), Gaps = 36/530 (6%) Query: 41 PASREAMIERL-RSEVFDLVVVGGGSTGAGCALDGATRGLKVALVDAGDFGSGTSSKSTK 99 P R ++ RL + +DL V+GGG+TG G ALD A RG V LVD+ DF GTSS++TK Sbjct: 9 PTQRADLLARLAQPHHYDLAVIGGGATGLGVALDAAARGFSVVLVDSHDFAKGTSSRATK 68 Query: 100 LVHGGVRYLAKAVSNLDWSQYKLVWQALGERTTMFEISPYLTNSIKIMVPIYSKILIPYY 159 LVHGGVRYLA+ LV +AL ERTT+ +P+L + ++P Y P+Y Sbjct: 69 LVHGGVRYLAQG-------NIALVREALHERTTLLHNAPHLAQPLPFVMPSYRFWETPFY 121 Query: 160 YVGLKLYDWISGFKSLGKSYFIDRKEAVDAFPHINKKNLCGAMVYFDGQQDDARNNVMIV 219 +GL +YD ++G LG + F+ R + P + L G + Y+DGQ DDAR + + Sbjct: 122 GIGLMMYDALAGKAGLGATQFLGRARTLACLPTARTEGLKGGVKYWDGQFDDARLALALA 181 Query: 220 MTAVCHGAVAANHVSARSLMIEGGKIVGVRCRDEITGSEIEIRGTGVINSTGNLADDLRR 279 TA GA+ N+ AR+L+ E GK+ G C D +G + +R V+N+TG D LR+ Sbjct: 182 RTAASLGALVVNYCPARALVHEAGKVAGFVCEDADSGQQFTVRARTVVNATGVWVDSLRQ 241 Query: 280 MD----DADAREIIVQSSGTHIVIPKEYAPKEMGFLDPLTSDNRIAFFMPWMGKTIVGST 335 MD + I+ S G HIV+ +E+ P + + P T+D R+ F +PW+GK I+G+T Sbjct: 242 MDGEAIGRPVKPIVAPSQGVHIVVDREFLPSDHALMVPKTADGRVLFAVPWLGKLILGTT 301 Query: 336 DIKTKTEL-SPSPTEEDLEFLIHEVQAYTSMHPKLTRDEVSAVWTGIRPLVK--DPDVSD 392 D + + P P E++ F++ E Y + PK +++ ++W G+RPLVK D D + Sbjct: 302 DSPRQDIVREPEPFREEVRFILEESARYLTRAPK--AEDIRSIWVGLRPLVKPQDDDGDN 359 Query: 393 TGSIVRKHFVRIEKNGLLTVTGGKWTIYRKMAEDAID--LAISAFSLKPSGPCVTKYVRI 450 T I R+H V ++GL+TVTGGKWT YR MAED + A KP+G VT + + Sbjct: 360 TKKISREHTVLASRSGLITVTGGKWTTYRAMAEDVLQKCFATGLLPTKPAG--VTNQLPL 417 Query: 451 LGGDGYTKNTWASIQKELGVPKNVAERLARSYGTRALRLSSYIKKNRKKVLSVKYSYLIE 510 +G A +Q + + + SYG+ A + + + VL + + Sbjct: 418 VG------TPQAPVQHRISDAQGL-----HSYGSEAAAVLAI--PGAQTVLGGGLTEAM- 463 Query: 511 EVEYCIDNEMAVKVCDVLCNRLMIGLMDVKEAYQCIDKVLGVFKKKHGWD 560 V + +E A V DVL R + +D ++A Q V G+ +++ G D Sbjct: 464 -VRFAARHEYACTVEDVLARRSRLLFLDARQAIQLAPVVAGILREELGGD 512 Lambda K H 0.320 0.136 0.404 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: 666 Number of extensions: 26 Number of successful extensions: 6 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: 614 Length of database: 530 Length adjustment: 36 Effective length of query: 578 Effective length of database: 494 Effective search space: 285532 Effective search space used: 285532 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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