Align β-galactosidase (BgalB) (EC 3.2.1.23) (characterized)
to candidate 352706 BT3179 beta-galactosidase (NCBI ptt file)
Query= CAZy::AAC24219.1 (1085 letters) >FitnessBrowser__Btheta:352706 Length = 1024 Score = 670 bits (1728), Expect = 0.0 Identities = 394/986 (39%), Positives = 549/986 (55%), Gaps = 56/986 (5%) Query: 4 EWENPQLVSEGTEKPHASFIPYLNPFT---GEWEYPDDFILLNGNWKFFFAKNPFEVPEN 60 EW++ V PH PY + G +E ++ LNG WKF + KNP P++ Sbjct: 32 EWQSQYAVGLNKLDPHTYVWPYADASEVEKGTFEQSPYYMSLNGQWKFHWVKNPDTRPKD 91 Query: 61 FFLEGFDDTNWDEIEVPSNWEMKGYGKPIYTNVVYPFEP-------NPPFVPKDDNPTGI 113 F+ + W +I+VP NWE +GYG IY N Y F+ NPP VP +N G Sbjct: 92 FYKPSYYTGGWADIKVPGNWERQGYGTAIYVNETYEFDDKMFNFKKNPPLVPYKENEVGS 151 Query: 114 YRRWVEVPEEWFEKEIFLHFEGVRSFFYLWVNGKRMGFSKDSCTPAEFRVTDVLKPGKNL 173 YRR +VP W + + L EGV SF+Y+WVNG+ +G+++ S T AE+ +TD L G+N Sbjct: 152 YRRTFKVPAGWEGRRVVLCCEGVISFYYVWVNGEFLGYNQGSKTAAEWDITDKLTDGENT 211 Query: 174 ICVEVLKWSDGSYLEDQDMWWFAGIYRDVYLYALSKFHVRDIFVRTDLD-EDYRDGKIFL 232 I +EV +WS G+YLE QDMW +GI RDVYLY+ + ++ D V + L+ E Y++G L Sbjct: 212 IALEVYRWSSGAYLECQDMWRLSGIERDVYLYSTPEQYIADYKVTSLLEKEHYKEGIFEL 271 Query: 233 DVELRNLGEEKEKDLIITLTDPQGKEMTLVEERVGPKNETLSFVFE---VKDPKKWSAET 289 +V + + TL D K + ++ VF+ + D ++W+AE Sbjct: 272 EVAVGGTA-SGTSSIAYTLKDASDKTVLEGSRKLESHGSGNLIVFDEQRLPDVRRWNAEH 330 Query: 290 PHLYVLKVELGEDEKKV------NFGFKKVEVKDGRLLFNGKPLYIKGVNRHEFDPDRGH 343 P LY L +EL + KV GF+ E+K+GR NG P+ +KGVNRHE G Sbjct: 331 PELYTLLLELKDAGGKVTEITGTKVGFRTSEIKNGRFCINGVPVLVKGVNRHEHS-QLGR 389 Query: 344 AVTVERMIQDIKLMKQHNINTVRTSHYPNQTKWYDLCDYYGLYVIDEANIESHGIGEAPE 403 V+ E M QDI+LMKQHNINTVR SHYP WY LCD YGLYVIDEANIESHG+G P Sbjct: 390 TVSKELMEQDIRLMKQHNINTVRNSHYPAHPYWYQLCDRYGLYVIDEANIESHGMGYGP- 448 Query: 404 VTLANRPEWEKAHLDRIKRMVERDKNHPSIIFWSLGNEAGDGMNFEKAALWIKERDNTRL 463 +LA W AH+DR +RM ER KNHPS++ WSLGNEAG+G+NFE+ W+K + R Sbjct: 449 ASLAKDSTWLPAHIDRTRRMYERSKNHPSVVIWSLGNEAGNGINFERTYDWLKSVEKNRP 508 Query: 464 VHYEGTTRRGESYYVDVFSLMYPKIDVLLEYASRKR-EKPFIMCEYAHAMGNSVGNLKDY 522 V YE R E+Y D++ MY +DV+ Y +RK +PFI+CEY HAMGNS G +K+Y Sbjct: 509 VQYE---RAEENYNTDIYCRMYRSVDVIRNYVARKDIYRPFILCEYLHAMGNSCGGMKEY 565 Query: 523 WDVIEKYPYLHGGCIWDWVDQGIRKKDENGKEFWAYGGDFG--DEPNDKNFCCNGVVLPD 580 W+V E P GGCIWDWVDQ R+ D++GK +W YGGD+G D P+ NFCCNG+V Sbjct: 566 WEVFENEPMAQGGCIWDWVDQSFREVDKDGKWYWTYGGDYGPKDVPSFGNFCCNGLVNAV 625 Query: 581 RTPEPELYEVKKFYQNIKVRQIAKD--TYEVENGYLFTDLEMFDGTWRIR-KDGEVVREE 637 R P P L EVKK YQNIK I K T V+N + F+DL + W++ DG V+ E Sbjct: 626 REPHPHLLEVKKIYQNIKSTLIDKKNLTVRVKNWFDFSDLNEYILHWKVTGDDGTVLAEG 685 Query: 638 RFKLSARPGEKKILKIPLPEMEDS--EYFLEICFSLSEDTLWAKKGHVVAWEQFLIKPPS 695 +++ P L + ++ + E +L++ ++ + T +A++QF++ P+ Sbjct: 686 NKEVACEPHATVELTLGAVQLPKTIREAYLDLGWTRKKSTPLVDTAWEIAYDQFVL--PA 743 Query: 696 FEKTVVRESVDLSEDGRHLFVRSKDTELVFSKFTGLLKRIVYRGRNILTGSIVPNFWRVP 755 K + SE G+ F ++ TG LK + G +L + + +R Sbjct: 744 SGKVWNGKP---SEAGKTTFEVDEN--------TGALKSLCLDGEELLASPVTISLFRPA 792 Query: 756 TDNDVGNKMPERLSIWKRASKERKLFKMFFWKKEENSVSVQ-SVYQVPGNSW--VYLTYT 812 TDND ++M +L W++A K+ K+ + S + Q ++ V G L YT Sbjct: 793 TDNDNRDRMGAKL--WRKAGLHTLTQKVVSLKESKTSATAQVNILNVTGKKVGDATLEYT 850 Query: 813 IFGNGDILVDLSLIP-AEGVPEIPRIGLQFAVPGDFRFVEWYGRGPHETYWDRKESGLFA 871 + NG + V + P V I R+GL F + + V + GRG HETY DR +SG Sbjct: 851 LNHNGSLKVQTTFQPDTTWVKSIARLGLTFEMNDTYGNVTYLGRGEHETYIDRNQSGKIG 910 Query: 872 RYRRTVQDMIHRYVRPQETGNRSDVRWFALSD--GRVNLFVSGMPVVDFSVWPFSMEDLE 929 Y T + M H YV PQ TGNR+DVRW L+D G+ S P FS PFS LE Sbjct: 911 IYTTTPEKMFHYYVIPQSTGNRTDVRWVKLADDSGKGCWIESDSP-FQFSALPFSDLLLE 969 Query: 930 KADHVNELPERDFVTVNVDYRQMGLG 955 KA H+N+L +TV++D +Q G+G Sbjct: 970 KALHINDLERNGRITVHLDAKQAGVG 995 Lambda K H 0.320 0.140 0.440 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: 3446 Number of extensions: 200 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: 1085 Length of database: 1024 Length adjustment: 45 Effective length of query: 1040 Effective length of database: 979 Effective search space: 1018160 Effective search space used: 1018160 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 (21.8 bits) S2: 58 (26.9 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