Align β-galactosidase (Gal4214-1) (EC 3.2.1.23) (characterized)
to candidate WP_066328382.1 BLR17_RS01125 DUF4981 domain-containing protein
Query= CAZy::AAX48919.1 (1046 letters) >NCBI__GCF_900100165.1:WP_066328382.1 Length = 1041 Score = 1000 bits (2586), Expect = 0.0 Identities = 492/1039 (47%), Positives = 665/1039 (64%), Gaps = 18/1039 (1%) Query: 12 IFAFISIIVFAQEKPSRNDWENPEVFQINREPARAAFLPFADEASAIADDYTRSPWYMSL 71 IFA + + + +N+WENP + + N+E R +F+ F +E +A + +S +Y SL Sbjct: 6 IFALLLAVQLINAQQQQNEWENPNIVERNKEAGRTSFVLFQNETTAATNQAEQSSYYKSL 65 Query: 72 DGKWKFNWSPTPDERPKDFFNTDFNTTTWKEIGVPSNWELVGYGIPIYTNITYPFVKNPP 131 DG+WKFN P +RP+DF+ D + +W I VPSNWEL G+ IPIYTNITYPF +NPP Sbjct: 66 DGEWKFNIVKKPIDRPQDFYKVDLDDKSWASIPVPSNWELQGFDIPIYTNITYPFPRNPP 125 Query: 132 FIDHADNPVGSYRRTFELPENWDGRRVYLHFEGGTSAMYVWINGEKVGYSQNTKSPTEFD 191 F+D+ NPVGSYR F +PENW+ + V LHF + V++NG++VG ++ K+ EFD Sbjct: 126 FVDNNYNPVGSYRTKFTVPENWNSKEVILHFGSISGYARVYLNGKEVGMTKAAKTAAEFD 185 Query: 192 ITKYVKVGKNQVAVEVYRWSDGSYLEDQDFWRLSGIDRSVYLYSTANTRIADFFARPDLD 251 +T +++ G+N +AV+V+RW DGSYLEDQDFWRLSGI+RSVYL + + D+F DLD Sbjct: 186 VTPFLQKGENVLAVQVFRWHDGSYLEDQDFWRLSGIERSVYLQAVPKLTVWDYFVHSDLD 245 Query: 252 TSYKNGSLSVDIKLKNANSVAKNNQTVEAKLVDAAGKEVFIKTIKINLGANTVSSTTFEQ 311 +Y NG ++L+ N + L+DA GK+V+ +T K++ N TF Sbjct: 246 ENYANGLFKTTVQLRAFQQNKIKNANLTLTLLDAQGKKVYAETKKVS---NLTKEVTFNS 302 Query: 312 MVKSPKLWNNETPNLYTLVLTLKDENGKFVETVATSIGFRKVELKNGQLLVNGIRIMVHG 371 V + W++E P LY ++ L+ N + GFRKVE+KN QLLVNG I++ G Sbjct: 303 TVTNVNKWSSEMPYLYRYIIKLESVNPDENSVIYGKTGFRKVEIKNAQLLVNGKAILIRG 362 Query: 372 VNIHEHNPKTGHYQDEATMMKDIKLMKQLNINAVRCSHYPNNLLWVKLCNKYGLFLVDEA 431 VN +H+ GH D TM KDI LMKQ NINA+R SHYP++ +LC++YG++++DEA Sbjct: 363 VNTQDHHETKGHTPDYPTMRKDIALMKQNNINAIRMSHYPHDPYLYQLCDEYGMYVIDEA 422 Query: 432 NIETHGMGAELQGSFDKTKHPAYLPEWKAAHMDRIYSLVERDKNQPSIILWSLGNECGNG 491 NIE+HGMG E Q ++KHP+Y+ W AH+DRI + E +KN PS+I+WS+GNECGNG Sbjct: 423 NIESHGMGVEGQNISAESKHPSYVSMWFPAHLDRIKRMFEINKNHPSVIIWSMGNECGNG 482 Query: 492 PVFHEAYNWIKNRDKTRLVQFEQAGEQENTDVVCPMYPSMEYMKEYANRKDVKRPFIMCE 551 PVFHEAY W+K+ D +R V EQA E NTD+V PMYP+++YMKEYA KD RPFIMCE Sbjct: 483 PVFHEAYKWLKSTDPSRPVHSEQAKENSNTDIVAPMYPTIKYMKEYAAAKDKTRPFIMCE 542 Query: 552 YSHAMGNSNGNFQEYWDIIHSSTNMQGGFIWDWVDQGFEETDEAGRKYWAYGGDMGGQNY 611 YSHAMGNS+GNFQEYWDII+SS +MQGGFIWDWVDQG + DE G Y+AYGGD+G ++ Sbjct: 543 YSHAMGNSSGNFQEYWDIINSSRHMQGGFIWDWVDQGIKTKDENGTVYYAYGGDLGSKDL 602 Query: 612 TNDQNFCHNGLVWPDRTPHPGAFEVKKVYQDILF--KGVNLDKGIIEVENGFGYTNLDKY 669 ND+NFC NGL+ +R PHPG EVKKVYQ ILF KG+N + ++N F YTNL++Y Sbjct: 603 RNDENFCDNGLISANRKPHPGLAEVKKVYQSILFSLKGLNQ----LTIKNIFQYTNLNQY 658 Query: 670 LFKFEVLKNGLVIKSGVINIRLAPQSKKQIQIELPKLTTEDGVEYLLNVFAYTKEGTELL 729 FKFE+ KNG +++ N+ P + + I+LP EY LNV+AYTK T+++ Sbjct: 659 QFKFELFKNGHLVQEKTFNVDCEP--GENVTIDLPVEALNANAEYFLNVYAYTKTATDMV 716 Query: 730 PQNFEIAREQFSIGESNYFV-KVAKASTNPIVKDSQDA--ITLSANGVEVTINKKTGLMQ 786 P N E+AREQF+IG+ N+F K + S +K A +T N V + + G+++ Sbjct: 717 PVNHEVAREQFAIGQGNFFAEKTMEISKKKDLKFKTKASVLTFETNAVAGSFDLSKGVLK 776 Query: 787 KYTS--GEENYFNQMPVPNFWRAPTDNDFGNYMQVNSNVWRTVGRFSSLDSIEV-KEVST 843 Y S P P FWRAPTDNDFGN M VW+ + S+ V K+ Sbjct: 777 SYISKNNPSEIVTAFPTPYFWRAPTDNDFGNKMPEKLVVWKEAHLNPEVKSVTVGKQTEQ 836 Query: 844 QTTVVAHLFLKDIASTYTITYSMDADGSLTLQNSFKAGEMALSEMPRFGMLFSLKKELDN 903 + L + Y + Y + +G + + S + + EMPRFGM L +N Sbjct: 837 GLPIDVEYALAEAKIPYIVNYLIQNNGEIKVTASIDVTDKKMPEMPRFGMRLELPGAYEN 896 Query: 904 FSYYGRGPWENYQDRNTSSLKGIYESKVADQYV-PYTRPQENGYKTDIRWITLTNSSGNG 962 SYYGRGP ENY DR ++S GIY+ KVA+Q+ Y RPQE G KTD RW +L N G G Sbjct: 897 LSYYGRGPLENYSDRKSASFVGIYQDKVANQFTWEYIRPQECGNKTDARWFSLQNDKGVG 956 Query: 963 IEILGLQPLGVSALNNYPEDFDPGLTKKQQHTNDITPRDEVIICVDLAQRGLGGDNSWGA 1022 ++I G QPL S LN E DPG TK Q+HTND+ P+D+V + +DLAQRGLGGD+SW + Sbjct: 957 LKITGEQPLSFSTLNVSTESLDPGKTKMQRHTNDVKPQDKVFVHLDLAQRGLGGDDSWKS 1016 Query: 1023 MPHEQYQLRNKAYSYGFVI 1041 +PHEQY L YSY + + Sbjct: 1017 LPHEQYLLTAPKYSYSYTL 1035 Lambda K H 0.316 0.134 0.410 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: 3330 Number of extensions: 183 Number of successful extensions: 7 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: 1046 Length of database: 1041 Length adjustment: 45 Effective length of query: 1001 Effective length of database: 996 Effective search space: 996996 Effective search space used: 996996 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 (21.6 bits) S2: 58 (26.9 bits)
This GapMind analysis is from Sep 24 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