Align β-galactosidase L+M (LacL+LacM) (EC 3.2.1.23) (characterized)
to candidate 352867 BT3340 beta-galactosidase (NCBI ptt file)
Query= CAZy::AAA25267.1 (626 letters) >FitnessBrowser__Btheta:352867 Length = 1036 Score = 407 bits (1047), Expect = e-118 Identities = 236/618 (38%), Positives = 334/618 (54%), Gaps = 34/618 (5%) Query: 10 DPEVFRVNQLPAHSDHHYYHDTAEFKTGSRF----IKSLNGAWRFNFAKTPAERPVDFYQ 65 DPEV VN+ H+++ Y E K GS+ +LNG W+FN+ + RP +FYQ Sbjct: 29 DPEVNSVNRSAMHTNYFAYASADEAKAGSKEDSQNFMTLNGLWKFNWVRNADARPTNFYQ 88 Query: 66 PDFDATDFDTIQVPGHIELAGYGQIQYINTLYPWEGKIYRRPPYTLNQDQLTPGLFSDAA 125 F+ +D I+VP EL GYG Y+N Y W + PP L P Sbjct: 89 TSFNDKGWDNIKVPAVWELNGYGDPIYVNVGYAWRNQFQNNPP-------LVP-----TE 136 Query: 126 DNTVGSYLKTFDLDDVFKGQRIIIQFQGVEEALYVWLNGHFIGYSEDSFTPSEFDLTPYI 185 +N VGSY K L +KG+ I F V +Y+W+NG ++GYSEDS +EFDLT Y+ Sbjct: 137 NNHVGSYRKEIVLPADWKGKDIFAHFGSVTSNMYLWVNGRYVGYSEDSKLEAEFDLTNYL 196 Query: 186 QDQGNVLAVRVYKHSTAAFIEDQDMFRFSGIFRDVNILAEPASHITDLDIRPVPNANLKS 245 + N++A +V++ +++EDQD FR+SG+ RD + A I D+ + P ++ K Sbjct: 197 KPGKNLIAFQVFRWCDGSYLEDQDFFRYSGVGRDCYLYARDKKRIQDIRVTPDLDSQYKD 256 Query: 246 GELNITTKVTGEPATLALTVKDHDGRVLTSQTQTGSGSVTFDTMLFDQLHLWSPQTPYLY 305 G LNI + G T+AL + D G+ + + GSG + T+ W+ +TP LY Sbjct: 257 GTLNIAIDMKGS-GTVALDLTDAQGKSVATADLKGSGKLN-TTINVANPAKWTAETPNLY 314 Query: 306 QLTIEVYDADHQLLEVVPYQFGFRTVELRDDKVIYVNNKRLVINGVNRHEWNAHTGRVIS 365 LT + + + EV+P + GFR +EL +++ VN + ++ G +RHE + G V+S Sbjct: 315 TLTATLKNGS-TVTEVIPVKVGFRKIELTGGQIL-VNGQPVLFKGADRHEMDPDGGYVVS 372 Query: 366 MADMRADIQTMLANNINADRTCHYPDQLPWYQLCDEAGIYLMAETNLESHGSWQKMGAIE 425 + M DI+ M NINA RTCHYPD WY LCD+ G+Y++AE N+ESHG MG + Sbjct: 373 LERMIQDIKVMKQLNINAVRTCHYPDDNRWYDLCDQYGLYVVAEANVESHG----MGYGD 428 Query: 426 PSYNVPGDNPHWPAAVIDRARSNYEWFKNHPSIIFWSLGNESYAGEDIAAMQAFYKEHDD 485 S NP + A ++R + N + NHPSIIFWSLGNE+ G + + K D Sbjct: 429 KSL---AKNPIYAKAHMERNQRNVQRGYNHPSIIFWSLGNEAGMGPNFEHCYTWIKNEDK 485 Query: 486 SRLVHYEGVFYTPELKDRISDVESRMYEKPQNIVAYLEDNPTKPFLNCEYMHDMGNSLGG 545 +R V YE +D+ MY N + Y E N KP + CEY H MGNS GG Sbjct: 486 TRAVQYEQAG-----TSEFTDIFCPMYYDYNNCIKYCEGNIDKPLIQCEYAHAMGNSQGG 540 Query: 546 MQSYNDLIDKYPMYQGGFIWDFIDQALFVHDPITDQDVLRYGGDFDERH-SDYAFSGNGL 604 + Y D+ KYP YQGGFIWDF+DQ+ + + YGGDF++ SD F+ NGL Sbjct: 541 FKEYWDITRKYPKYQGGFIWDFVDQSCHWKNK-DGVAIYGYGGDFNKYDASDNNFNDNGL 599 Query: 605 MFADRTPKPAMQEVKYYY 622 + DR P P EV Y+Y Sbjct: 600 ISPDRVPNPHAYEVGYFY 617 Lambda K H 0.320 0.138 0.430 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: 1899 Number of extensions: 107 Number of successful extensions: 9 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: 1036 Length adjustment: 41 Effective length of query: 585 Effective length of database: 995 Effective search space: 582075 Effective search space used: 582075 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: 56 (26.2 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