Align Beta-glucosidase (EC 3.2.1.21) (characterized)
to candidate N515DRAFT_3019 N515DRAFT_3019 beta-glucosidase
Query= reanno::Caulo:CCNA_01019 (758 letters) >lcl|FitnessBrowser__Dyella79:N515DRAFT_3019 N515DRAFT_3019 beta-glucosidase Length = 737 Score = 719 bits (1856), Expect = 0.0 Identities = 373/718 (51%), Positives = 476/718 (66%), Gaps = 15/718 (2%) Query: 39 AHPWMDKSLDADKRADLVLKAMTNDEKFTLIFGYFGADMKPKYTRIPESLPGSAGYIAGV 98 A PW D L D RAD +L +T DEKF LI YF KP+ +P GSAGYI + Sbjct: 31 ARPWSDPKLSPDLRADQLLAQLTQDEKFHLIRSYFAGPRKPEDKPVPPGYIGSAGYIPAL 90 Query: 99 PRLGIPAQFQTDAGVGVATQGSAKEFRERTALPSGMATTATWNPELAFQGGAMIGKEARD 158 R+GIPA ++DAG+GVA+ + T LP+G T ATW+P++AF+GGAMIG EA Sbjct: 91 ERVGIPAIQESDAGLGVASSERMRPGDYATPLPAGPVTAATWDPKVAFRGGAMIGGEAHA 150 Query: 159 SGFNVQLAGGVNLVREPRNGRNFEYGGEDPLLAGVMVAAQIRGIQSNNIISTIKHYALNA 218 GFNV LAGG NL+REPRNGRNFEY GEDPLLAG MV IRGI+S +++STIKH+ALN Sbjct: 151 KGFNVLLAGGTNLMREPRNGRNFEYAGEDPLLAGTMVGEAIRGIESQHVVSTIKHFALND 210 Query: 219 QETGRFVVSSNIDDTAARMSDLLAFQFAIEQSDPHSVMCAYNRVNSVYACESDWLLNTVL 278 QET R V I + A R SDLLAF+ AIE+ P SVMC+YN++N +ACE+D+LLN VL Sbjct: 211 QETARTTVDVRIGEQAMRESDLLAFELAIERGKPGSVMCSYNKLNGDWACENDYLLNQVL 270 Query: 279 KKDWGYKGYVMSDWGAAHSSAKAANAGLDQESAGDAFDKQPFFAAPLKADLASGAVSQAR 338 K+DW Y G+VMSDWG HS+AKA NAGLDQESA + FDK +F PL+ LA G V QAR Sbjct: 271 KRDWKYPGFVMSDWGGVHSAAKAVNAGLDQESAAEIFDKDIYFDKPLRDALAKGEVKQAR 330 Query: 339 IDDMARRVLRAMFASGVVDHPLTGAPLAMPAETLAAHAKITQADAEEGIVLLKNDGGLLP 398 IDDM RR+LR+ FA+GV +HP AP+ A A + E G VLL+ND LLP Sbjct: 331 IDDMVRRILRSFFAAGVFEHPAKKAPIDEKANLAVARETL-----EAGAVLLRNDNQLLP 385 Query: 399 L-AKTAKTIAVIGSYADVGVLSGGGSSQVYPVGGRAVQGLEPKTWPGPVIYYPSSPLKAI 457 L ++IAVIG++AD GVL+GGGSS V GG AV GL+P WPGPV+Y+P SPLKA+ Sbjct: 386 LDVARLESIAVIGAHADKGVLAGGGSSLVTAKGGNAVPGLKPSDWPGPVMYHPYSPLKAL 445 Query: 458 AARYPGAKVVYDDGTDPARAAKLAASSDLALVFADQWTTESVDVTTLNLPKNQDATIDAV 517 + P AKV + G D A AA LAA S +A+VF +W E D L+LP QDA + AV Sbjct: 446 QSMAPKAKVQFTGGDDVAAAAALAAKSQVAVVFVQKWAGEDFDARDLSLPDGQDALVTAV 505 Query: 518 ASANKKTVVVLLTGGPLLMPWLDKVGAVVEAWFPGTAGGEAIARVLTGEVDASGRLPVTF 577 A AN +T+VVL G P+ MPWL++VGAV+E W+PG G IA +L+G+V+ SGRLP+++ Sbjct: 506 AKANPRTIVVLENGSPVAMPWLEQVGAVLEVWYPGGDAGNGIANLLSGKVNPSGRLPLSW 565 Query: 578 PKSVAELPRPKLDGLGKPDGEMFDVDYTLEGAAVGYKWYDLKKIEPLFAFGHGLSYTQFA 637 P+ V +LPRP+L G G VDY +EGA VGY+WY K ++PLF FG+GLSYT F Sbjct: 566 PRDVLQLPRPELPGAGGSGALPQSVDYAIEGANVGYRWYQSKDLQPLFPFGYGLSYTSFE 625 Query: 638 YSNLTASASGDTLTVSFEVKNVGRRPGKDVPQVYV---GPKAGGWEAPKRLAGFQKVSLA 694 + L +T + V+N G+R G DV QVYV G KA +RLAGF KV L Sbjct: 626 HGALKVDTKDGKVTATVTVRNTGKRAGADVAQVYVQVPGAKA------RRLAGFSKVFLK 679 Query: 695 PGASQRVTVTVDPRLLAVWDSKAHGWSIAAGQYDIALGASSRAISSTAQVTLAARSLP 752 PG + +++ ++ +LLA +D+ HGW + G+Y ++ G SS + A V L+A LP Sbjct: 680 PGEQRELSIPLERKLLADFDTARHGWVVRGGEYVVSEGRSSADLGRPAAVQLSAGVLP 737 Lambda K H 0.316 0.131 0.385 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: 1469 Number of extensions: 67 Number of successful extensions: 4 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: 758 Length of database: 737 Length adjustment: 40 Effective length of query: 718 Effective length of database: 697 Effective search space: 500446 Effective search space used: 500446 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: 55 (25.8 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