Align β-galactosidase (Gal4214-1) (EC 3.2.1.23) (characterized)
to candidate 352867 BT3340 beta-galactosidase (NCBI ptt file)
Query= CAZy::AAX48919.1 (1046 letters) >lcl|FitnessBrowser__Btheta:352867 BT3340 beta-galactosidase (NCBI ptt file) Length = 1036 Score = 761 bits (1964), Expect = 0.0 Identities = 426/1062 (40%), Positives = 593/1062 (55%), Gaps = 54/1062 (5%) Query: 5 KRTILTSIFAFISIIVFAQEKPSRNDWENPEVFQINREPARAAFLPFADEASAIADDYTR 64 K+ +L+ A + + Q + + N+W++PEV +NR + +A A A Sbjct: 2 KKQLLSCCLAALGLTTAIQAQ-NFNEWKDPEVNSVNRSAMHTNYFAYASADEAKAGSKED 60 Query: 65 SPWYMSLDGKWKFNWSPTPDERPKDFFNTDFNTTTWKEIGVPSNWELVGYGIPIYTNITY 124 S +M+L+G WKFNW D RP +F+ T FN W I VP+ WEL GYG PIY N+ Y Sbjct: 61 SQNFMTLNGLWKFNWVRNADARPTNFYQTSFNDKGWDNIKVPAVWELNGYGDPIYVNVGY 120 Query: 125 P----FVKNPPFIDHADNPVGSYRRTFELPENWDGRRVYLHFEGGTSAMYVWINGEKVGY 180 F NPP + +N VGSYR+ LP +W G+ ++ HF TS MY+W+NG VGY Sbjct: 121 AWRNQFQNNPPLVPTENNHVGSYRKEIVLPADWKGKDIFAHFGSVTSNMYLWVNGRYVGY 180 Query: 181 SQNTKSPTEFDITKYVKVGKNQVAVEVYRWSDGSYLEDQDFWRLSGIDRSVYLYSTANTR 240 S+++K EFD+T Y+K GKN +A +V+RW DGSYLEDQDF+R SG+ R YLY+ R Sbjct: 181 SEDSKLEAEFDLTNYLKPGKNLIAFQVFRWCDGSYLEDQDFFRYSGVGRDCYLYARDKKR 240 Query: 241 IADFFARPDLDTSYKNGSLSVDIKLKNANSVAKNNQTVEAKLVDAAGKEVFIKTIKINLG 300 I D PDLD+ YK+G+L++ I +K + +VA + L DA GK V +K G Sbjct: 241 IQDIRVTPDLDSQYKDGTLNIAIDMKGSGTVALD-------LTDAQGKSVATADLK---G 290 Query: 301 ANTVSSTTFEQMVKSPKLWNNETPNLYTLVLTLKDENGKFV-ETVATSIGFRKVELKNGQ 359 + +++T V +P W ETPNLYTL TLK NG V E + +GFRK+EL GQ Sbjct: 291 SGKLNTTI---NVANPAKWTAETPNLYTLTATLK--NGSTVTEVIPVKVGFRKIELTGGQ 345 Query: 360 LLVNGIRIMVHGVNIHEHNPKTGHYQDEATMMKDIKLMKQLNINAVRCSHYPNNLLWVKL 419 +LVNG ++ G + HE +P G+ M++DIK+MKQLNINAVR HYP++ W L Sbjct: 346 ILVNGQPVLFKGADRHEMDPDGGYVVSLERMIQDIKVMKQLNINAVRTCHYPDDNRWYDL 405 Query: 420 CNKYGLFLVDEANIETHGMGAELQGSFDKTKHPAYLPEWKAAHMDRIYSLVERDKNQPSI 479 C++YGL++V EAN+E+HGMG G K+P Y AHM+R V+R N PSI Sbjct: 406 CDQYGLYVVAEANVESHGMG---YGDKSLAKNPIY----AKAHMERNQRNVQRGYNHPSI 458 Query: 480 ILWSLGNECGNGPVFHEAYNWIKNRDKTRLVQFEQAGEQENTDVVCPMYPSMEYMKEYAN 539 I WSLGNE G GP F Y WIKN DKTR VQ+EQAG E TD+ CPMY +Y Sbjct: 459 IFWSLGNEAGMGPNFEHCYTWIKNEDKTRAVQYEQAGTSEFTDIFCPMYYDYNNCIKYC- 517 Query: 540 RKDVKRPFIMCEYSHAMGNSNGNFQEYWDIIHSSTNMQGGFIWDWVDQGFEETDEAGRKY 599 ++ +P I CEY+HAMGNS G F+EYWDI QGGFIWD+VDQ ++ G Sbjct: 518 EGNIDKPLIQCEYAHAMGNSQGGFKEYWDITRKYPKYQGGFIWDFVDQSCHWKNKDGVAI 577 Query: 600 WAYGGDMGGQNYTNDQNFCHNGLVWPDRTPHPGAFEVKKVYQDILFKGVNLDKGIIEVEN 659 + YGGD + +D NF NGL+ PDR P+P A+EV YQ+I +L KG I + N Sbjct: 578 YGYGGDFNKYD-ASDNNFNDNGLISPDRVPNPHAYEVGYFYQNIWTTPADLSKGEINIYN 636 Query: 660 GFGYTNLDKYLFKFEVLKNGLVIKSGVI-NIRLAPQSKKQIQIELPKLTTEDGVEYLLNV 718 + +L + ++++L NG +I++G++ ++ +APQ ++Q+ E LLNV Sbjct: 637 ENFFRDLSAFYLEWQLLANGEIIQNGIVSDLNVAPQQTAKLQLPFDIKNICSCKELLLNV 696 Query: 719 FAYTKEGTELLPQNFEIAREQFSIGE-------------SNYFVKVAKASTNPIVKDSQD 765 K LLP IA +Q SI + SN V V N + Sbjct: 697 SYKLKAAETLLPAGETIAYDQMSIRDYKAPELKLENKQSSNIAVVVPSFQDN-----DHN 751 Query: 766 AITLSANGVEVTINKKTGLMQKY-TSGEENYFNQMPV-PNFWRAPTDNDFGNYMQVNSNV 823 + +S + NK G + +Y SG + + + PNFWRAPTDNDFG +Q Sbjct: 752 YLIVSGEDFTLEFNKHNGYLCRYDVSGTQLMEDGSALTPNFWRAPTDNDFGAGLQHRYGA 811 Query: 824 WRTVGRFSSLDSIEVKEVSTQTTVVAHLFLKDIASTYTITYSMDADGSLTLQNSFKAGE- 882 W+ L S++ + Q V A +K I +TY+++ G++ + +A + Sbjct: 812 WKNPE--LKLTSLKHDIENEQAVVRAEYDMKSIGGKLFLTYAINNKGAVKVTQKMEADKS 869 Query: 883 MALSEMPRFGMLFSLKKELDNFSYYGRGPWENYQDRNTSSLKGIYESKVADQYVPYTRPQ 942 +S+M RFGM + + YYGRGP ENY DRN ++ G Y V +Q+ PY RPQ Sbjct: 870 KKVSDMFRFGMQLRMPVTFNEIEYYGRGPGENYSDRNHAARIGKYRQTVEEQFYPYIRPQ 929 Query: 943 ENGYKTDIRWITLTNSSGNGIEILGLQPLGVSALNNYPEDFDPGLTKKQQHTNDITPRDE 1002 E G KTDIRW L N GNG++ + P SALN E D G K Q+H+ ++ + Sbjct: 930 ETGTKTDIRWWRLLNIGGNGLQFVADAPFSASALNYTIESLDDGAGKDQRHSPEVEKANF 989 Query: 1003 VIICVDLAQRGLGGDNSWGAMPHEQYQLRNKAYSYGFVIKPI 1044 C+D Q GL NSWGA+ E+Y+L + Y + F++ P+ Sbjct: 990 TNFCIDKVQTGLACVNSWGAIALEKYRLPYQDYEFSFIMNPV 1031 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: 3250 Number of extensions: 195 Number of successful extensions: 12 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: 1036 Length adjustment: 45 Effective length of query: 1001 Effective length of database: 991 Effective search space: 991991 Effective search space used: 991991 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: 57 (26.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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