Align β-galactosidase (LacLM;LacL+LacM) (EC 3.2.1.23) (characterized)
to candidate 352820 BT3293 beta-galactosidase (NCBI ptt file)
Query= CAZy::AEJ32720.1 (626 letters) >FitnessBrowser__Btheta:352820 Length = 1421 Score = 388 bits (997), Expect = e-112 Identities = 219/615 (35%), Positives = 329/615 (53%), Gaps = 45/615 (7%) Query: 28 YRDQEEA---ALEKSSYVQNLNGRWGFKFSKNPMERPVDFYKLDFDRNDFGEIEVPSEIE 84 + D+++A +E+S Y + LNG W F + +P +RP DF K ++D + + I+VP+ + Sbjct: 50 FTDEQQAMNLTIEESPYYKTLNGIWKFHWVADPKDRPQDFCKPEYDVSQWDNIKVPATWQ 109 Query: 85 LS------NFAQINYTNITMP----------WTGKIYRRPA-YTLGDNKEEGSFSQGKDN 127 + N+ + Y N+ P W I RP+ YT N Sbjct: 110 IEAVRHNKNWDKPLYCNVIYPFCEWDWKKIQWPNVIQPRPSNYTFAT----------MPN 159 Query: 128 TVGSYVRHFTLAEGLKNHDVHVVFEGVERAMYVWLNGHFIGYAEDSFTPSEFDLTPYLVD 187 VGSY R F L + K D+ + F GVE Y+W+NG +GY+EDS+ P+EF+LTPYL Sbjct: 160 PVGSYRREFILPDSWKGRDIFIRFNGVEAGFYIWVNGKKVGYSEDSYLPAEFNLTPYLKA 219 Query: 188 GDNLLAVEVYKHATSSWIEDQDMFRFSGIFRDVNLVAQPSIHVQDLKIDARVADDMKTGS 247 G N+LAVEVY+ S++E QD +RFSGIFRDV L + P ++D + + K S Sbjct: 220 GKNVLAVEVYRFTDGSFLECQDFWRFSGIFRDVFLWSAPKTQIRDFFFRTDLDKEYKNAS 279 Query: 248 LGLVLKVVGQPGS--VQVEVADQTGAAVLNRQLNADGNWTMAPVQLVGIHLWDNHHPYLY 305 + L + + G+ + +QV+V DQ G + + A ++V W P LY Sbjct: 280 VSLDIDITGKRSNNEIQVKVTDQNGKEIATQNARAVTGTNKLQFEVVNPLKWTAETPNLY 339 Query: 306 QLTLTVRDATGRVVEVIPYQFGFRRVEIDQDKVLRLNGKRLIINGVNRHEWNCHRGRAVT 365 LT+ ++ G+ V++ + GFR++E+ QD L +NGK + GV+RH+ + GR V+ Sbjct: 340 NLTILLKQ-KGKTVDIRSVKVGFRKIELAQDGRLLINGKSTLFKGVDRHDHSSENGRTVS 398 Query: 366 IEDMHTDLGIFKENNINAVRTSHYPDQIPWYYLCDREGIYMMAENNLESHATWQKFGQDE 425 E+M D+ + K NINAVRTSHYP+ +Y LCDR GIY+++E N+E H Sbjct: 399 KEEMEKDVQLMKSLNINAVRTSHYPNNPYFYDLCDRYGIYVLSEANVECHGLM------- 451 Query: 426 PSYNVPGSLPQWKEAVVDRARSNYETFKNHTAILFWSVGNESYAGEDILAMNNYYKEVDD 485 S P W +A +R+ + +KNH +I+ WS+GNES G + + K++DD Sbjct: 452 ----ALSSEPSWVKAFTERSENMVRRYKNHASIVMWSLGNESGNGINFKSAAEAVKKLDD 507 Query: 486 TRPVHYEGVVHTKEYRDQISDFESWMYLPPKE-VEAYLKKNPDKPFIECEYMHSMGNSVG 544 TRP HYEG + + W+ KE ++ + KP + CEY H+MGNS+G Sbjct: 508 TRPTHYEGNSSYCDVTSSMYPDVQWLESVGKERLQKFQNGETVKPHVVCEYAHAMGNSIG 567 Query: 545 GMDSYIKLLDKYPQYCGGFIWDFVDQAIEVVDPVTGQKSMRYGGDFDDHHADNEFSGDGI 604 Y + ++YP GGFIWD+VDQ+I++ P M +GGDF D D F +G+ Sbjct: 568 NFKEYWETYERYPALVGGFIWDWVDQSIKMPAPDGSGYYMAFGGDFGDTPNDGNFCTNGV 627 Query: 605 CFADRTPKPAMQEVK 619 F+DRT EVK Sbjct: 628 IFSDRTYSAKAYEVK 642 Lambda K H 0.319 0.137 0.428 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: 2477 Number of extensions: 131 Number of successful extensions: 6 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: 626 Length of database: 1421 Length adjustment: 44 Effective length of query: 582 Effective length of database: 1377 Effective search space: 801414 Effective search space used: 801414 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 (21.7 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:
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