Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate HSERO_RS22235 HSERO_RS22235 short-chain dehydrogenase
Query= reanno::Smeli:SMc02322 (699 letters) >FitnessBrowser__HerbieS:HSERO_RS22235 Length = 690 Score = 972 bits (2512), Expect = 0.0 Identities = 467/690 (67%), Positives = 565/690 (81%) Query: 10 LANLWDDGKAAGMTEPEKLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLTGEIVEVLWV 69 +A+ WD+ AA + EP+ LLYRSNLLG+DK ITN+GGGNTSAK+ DPLTG+ VEVLWV Sbjct: 1 IASAWDEAYAATLDEPQLLLYRSNLLGADKEITNFGGGNTSAKIAMPDPLTGQTVEVLWV 60 Query: 70 KGSGGDVGTIKMDGFSTLYMDKLRALKGIYRGVEFEDEMVGYLPHCTFNLNPRAASIDTP 129 KGSGGD+G+IK+DGF+TLYMDKL AL+ YRG+E EDEMVGYLPHCT+NLN RAASIDTP Sbjct: 61 KGSGGDLGSIKLDGFATLYMDKLEALRSRYRGLEHEDEMVGYLPHCTYNLNARAASIDTP 120 Query: 130 LHAYVPKPHVDHMHPDAIIAIAASKNSRELTSKIFGDEIGWLPWKRPGYELGLWLEKFCQ 189 LHAY+P+ HVDHMHPDA+IAIAA KNSR+LT++IF E+GWLPW+RPGY+LGL LE+ + Sbjct: 121 LHAYIPRRHVDHMHPDAVIAIAACKNSRDLTARIFEGELGWLPWQRPGYDLGLKLEQLVR 180 Query: 190 ENPDARGVVLESHGLFTWGDTAKEAYETTIEIINRAIAWFETENTGPAFGGRSKPVLAAA 249 P +G+VLE HGLFTWGD+A+E YE T+ +I RA AW + PAFGG L A Sbjct: 181 AQPHLKGIVLEGHGLFTWGDSARECYENTLNVIRRADAWLAANSRTPAFGGARYQALPKA 240 Query: 250 DRAAIAKKLMPVIRGLISAGESKVGHFDDSQAVLDFVTSTSLEPLAALGTSCPDHFLRTK 309 +RAA+A ++MP++RG IS GE K+GHFDDSQAVLDFV S L LAALGTSCPDHFLRTK Sbjct: 241 ERAALAARIMPLLRGKISKGEYKLGHFDDSQAVLDFVCSNDLAALAALGTSCPDHFLRTK 300 Query: 310 IRPLVVDFDPAQPDVGNTLAGLPEAIATYRADYAAYYERCKRADSPAMRDPNAVVYLVPG 369 IRPLV+DF P QPD+ A L A+ YR DYAAYY+RC R +SPAMRDPN V+YL+PG Sbjct: 301 IRPLVLDFSPQQPDLAALEASLDAALEAYRQDYAAYYQRCARPNSPAMRDPNPVIYLIPG 360 Query: 370 VGMITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWLLEEAKLQRM 429 VGM++FAKDKATARI+ EFY+NA+NVMRGA+GV +YVGLPEQEAFDIEYWLLEEAKLQRM Sbjct: 361 VGMLSFAKDKATARIAGEFYINAVNVMRGANGVDSYVGLPEQEAFDIEYWLLEEAKLQRM 420 Query: 430 PKPKSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDETALEAAQTELSTRYGKDF 489 PKPKSLAGRIALVTGG GGIG+A A +L+ EGACV+L DID++AL++AQ L G D Sbjct: 421 PKPKSLAGRIALVTGGGGGIGQAVARQLLAEGACVMLTDIDQSALDSAQQSLLKHGGPDA 480 Query: 490 VRSVNMNVTSEAAVESGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALWNKNMDILAT 549 + V ++TSEA V + L FGG+D+LVSNAG+A+++ ++DT+L +W +N+ +LAT Sbjct: 481 IGVVRADITSEADVTTILNSVALRFGGIDLLVSNAGIASASPLQDTSLEVWQRNLSVLAT 540 Query: 550 GYFLVSREAFRIFRNQKAGGNVVFVASKNGLAASPGASAYCTAKAAEIHLARCLALEGAS 609 GYFLVSR AF Q GG++V+VASKNGL AS GASAYCTAKAAEIHLARC+ALEGA Sbjct: 541 GYFLVSRAAFSSMLTQGLGGSIVYVASKNGLVASAGASAYCTAKAAEIHLARCIALEGAP 600 Query: 610 AQIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMDVDELEAHYRERSMLKLSVFPEDIAE 669 IRVNVVNPDAV+RGS+IW G+WKE+RAA+ K++ D++E YR+RSMLK SV PEDIAE Sbjct: 601 HGIRVNVVNPDAVIRGSRIWDGKWKEERAASNKIEADDVEEFYRQRSMLKRSVLPEDIAE 660 Query: 670 AIYFLASDMSAKSTGNIVNVDAGNAQSFTR 699 A+YF AS+ SAKSTGNI+NVDAGNA +FTR Sbjct: 661 AVYFFASEKSAKSTGNILNVDAGNAGAFTR 690 Lambda K H 0.317 0.133 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: 1303 Number of extensions: 36 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: 699 Length of database: 690 Length adjustment: 39 Effective length of query: 660 Effective length of database: 651 Effective search space: 429660 Effective search space used: 429660 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: 54 (25.4 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