Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate GFF2991 PGA1_c30400 alcohol dehydrogenase AlkJ
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Phaeo:GFF2991 Length = 529 Score = 632 bits (1629), Expect = 0.0 Identities = 333/544 (61%), Positives = 391/544 (71%), Gaps = 23/544 (4%) Query: 35 AFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWR 94 ++DYI+VGAG+AGC+LANRLSA RVLL+EAGG+DNYHW+HIP+GYLYCINNPRTDW Sbjct: 2 SWDYIIVGAGSAGCVLANRLSA-AGQRVLLLEAGGKDNYHWVHIPMGYLYCINNPRTDWM 60 Query: 95 FRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLP 154 +RTE + GLNGR+LIYPRGK LGGCSSINGMLYLRGQA DYDGW + G W WD+ LP Sbjct: 61 YRTEAEAGLNGRALIYPRGKVLGGCSSINGMLYLRGQAADYDGWRQ-RGLTGWGWDDVLP 119 Query: 155 DFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRD 214 F + ED+ G +D HG GGEWR+E QRL W VL D+ AA E G+P+ D Sbjct: 120 YFKKSEDYV----DGSSD-----MHGVGGEWRVENQRLHWDVLDDWMQAAAEWGLPKVTD 170 Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPR 274 FN G+NEGV F VNQRSGWR N +KAFLR NL V ++ +G R Sbjct: 171 FNTGNNEGVGYFRVNQRSGWRMNTAKAFLRTATGE-NLKVETGAHTRRILIENG-----R 224 Query: 275 CCGVTVERAGKKVVTTARC--EVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPG 332 GV + G V TAR EV+LSAGAI SPQ+LQLSG+GP ALL +H I V D+P Sbjct: 225 AVGVEYSQGG--AVKTARTGGEVLLSAGAINSPQILQLSGLGPEALLRDHGIAVQRDMPE 282 Query: 333 VGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTR 392 VG+NLQDHLQ+R +++KGAKTLNT+ANSLIGKAKI EY ++RSGPMSMAPSQL F+R Sbjct: 283 VGQNLQDHLQLRCAWRLKGAKTLNTLANSLIGKAKIAAEYAMRRSGPMSMAPSQLGAFSR 342 Query: 393 SSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAI 452 S + P+LEYHVQPL+LEAFGQPLHDFP +TASVCNL P SRG V I S +P QAP I Sbjct: 343 SRPDLATPDLEYHVQPLTLEAFGQPLHDFPGLTASVCNLRPESRGEVAITSADPMQAPRI 402 Query: 453 SPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTT 512 +PNYLSTE DRQVA ++R R I Q A +Y P E KPG DL + AG IGTT Sbjct: 403 APNYLSTEGDRQVAVAAIRQARAIMGQEAMQRYAPVEMKPGGGSDEAADLMQAAGAIGTT 462 Query: 513 IFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAA 572 IFHP T +MG ++ A VD LR+RGV GLRVVDAS+MP I SGNTN+PT+MIAEKAA Sbjct: 463 IFHPTCTLRMGAEE--AAPVDGALRLRGVGGLRVVDASVMPVIPSGNTNAPTIMIAEKAA 520 Query: 573 GWIL 576 IL Sbjct: 521 DMIL 524 Lambda K H 0.318 0.135 0.418 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: 956 Number of extensions: 35 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: 579 Length of database: 529 Length adjustment: 36 Effective length of query: 543 Effective length of database: 493 Effective search space: 267699 Effective search space used: 267699 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: 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