Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate PP_1949 PP_1949 Oxidoreductase, GMC family
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Putida:PP_1949 Length = 550 Score = 389 bits (1000), Expect = e-112 Identities = 223/535 (41%), Positives = 315/535 (58%), Gaps = 26/535 (4%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 +DY+I+GAGSAGCVLANRLSA+P +V LLEAG + P G++ ++ NWA+ Sbjct: 8 YDYIIIGAGSAGCVLANRLSANPEHSVLLLEAGSRPKGLWASMPAGVSRVILPGPTNWAY 67 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 ++ P P L GR Y PRGK LGGSS+INGM Y+RGH++D++ W +LG GWG+DDVLP++ Sbjct: 68 QSEPDPSLAGRRIYVPRGKALGGSSAINGMAYLRGHREDYDHWVSLGCAGWGWDDVLPFY 127 Query: 123 RKSEMHHGGSSEYHGGDGELYVS-PANRHAASEAFVESALRAGHSYNPDFNGATQEGAGY 181 +K E G + G DGEL+V+ P +H +S+AF+ES + AG D N + EG G+ Sbjct: 128 KKFEHREEGDEAFRGRDGELWVTDPVFKHPSSQAFIESCVEAGIPRLDDLNAPSPEGTGF 187 Query: 182 YDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLR 241 TI+ GRR S ATAFL+PV R NL VLT V+ IV+ ++ATGV+ + G++ Sbjct: 188 LQFTIKGGRRHSAATAFLQPVLKRPNLHVLTGALVQKIVIEAERATGVEYSL-GNQSIFA 246 Query: 242 ARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSN 301 A +E+ILSAGA SP LLMLSG+G A EL GI +LPGVG+NL DH V +++ Sbjct: 247 AAREIILSAGAIDSPKLLMLSGVGPAQELTRHGIPVLRDLPGVGENLHDHVYVHSGIETD 306 Query: 302 DTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIGT 361 + L L G + + M +Y G + ++A A + PG RPD Q+ Sbjct: 307 RVASLNKDLRGLRSVLQGM-NYLLRGKGCLTMGASQAVALAQVLPGARRPDTQI------ 359 Query: 362 VDDHNRKLHW------------GHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLA 409 + R L W + + C L P S G + L S +P AP I PN+ Sbjct: 360 ---NYRPLSWHFNKQGLVEIGKDNAVTISTCQLNPLSRGRLTLKSSNPIDAPAIYPNYFG 416 Query: 410 HDDDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKR-TDTIYHPIG 468 ++ D+ + R R+I P+A + ++ +D ++ + +R+ ++ H +G Sbjct: 417 NERDMVAAIAAVRKVREISCVGPLAKH-IVNISPPDSMSDGEIADYIRQEGASSMMHWVG 475 Query: 469 TCKMGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 +CKMG D MAVVD +L+V G++GLRVVDASIMPT+ GNTNA IMI E+ A I Sbjct: 476 SCKMGIDSMAVVDERLKVRGLQGLRVVDASIMPTITSGNTNAPTIMIGEKGAAMI 530 Lambda K H 0.319 0.137 0.419 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: 777 Number of extensions: 39 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: 526 Length of database: 550 Length adjustment: 35 Effective length of query: 491 Effective length of database: 515 Effective search space: 252865 Effective search space used: 252865 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 (21.7 bits) S2: 52 (24.6 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