Align β-galactosidase (LacL+LacM) (EC 3.2.1.23) (characterized)
to candidate 14482 b0344 beta-D-galactosidase (NCBI)
Query= CAZy::CAZ66936.1 (626 letters) >FitnessBrowser__Keio:14482 Length = 1024 Score = 357 bits (917), Expect = e-102 Identities = 227/641 (35%), Positives = 334/641 (52%), Gaps = 64/641 (9%) Query: 9 DDPEVFRVNQLPAHSDHHYYHDTAEFKTG--SRFIKSLNGAWRFNFAKTPAERPVDFYQP 66 ++P V ++N+L AH + ++ E +T S+ ++SLNG WRF + P P + + Sbjct: 18 ENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLEC 77 Query: 67 DFDATDFDTIQVPGHIELAGYGQIQYINTLYPWEGKIYRRPPYTLNQDQLTPGLFSDAAD 126 D + DT+ VP + ++ GY Y N YP I PP+ + Sbjct: 78 DLP--EADTVVVPSNWQMHGYDAPIYTNVTYP----ITVNPPFV-------------PTE 118 Query: 127 NTVGSYLKTFDLDDAF--KGQRIIIQFQGVEEALYVWLNGHFIGYAEDSFTPSEFDLTPY 184 N G Y TF++D+++ +GQ II F GV A ++W NG ++GY +DS PSEFDL+ + Sbjct: 119 NPTGCYSLTFNVDESWLQEGQTRII-FDGVNSAFHLWCNGRWVGYGQDSRLPSEFDLSAF 177 Query: 185 IQDQGNVLAVRVYKRSTAAFIEDQDMFRFSGIFRDVNILAEPASHITDLDIRPVPNANLK 244 ++ N LAV V + S +++EDQDM+R SGIFRDV++L +P + I+D + N + Sbjct: 178 LRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFS 237 Query: 245 SGELNITTKVTGEPAT-LALTVKDHDGRVLTSQTQTGSGSVTFDTMLFDQL--------- 294 L ++ GE L +TV G +TQ SG+ F + D+ Sbjct: 238 RAVLEAEVQMCGELRDYLRVTVSLWQG-----ETQVASGTAPFGGEIIDERGGYADRVTL 292 Query: 295 -------HLWSPQTPYLYQLTIEVYDADRQLLEVVPYQFGFRTVELRDDKVIYVNNKRLV 347 LWS + P LY+ +E++ AD L+E GFR V + ++ ++ +N K L+ Sbjct: 293 RLNVENPKLWSAEIPNLYRAVVELHTADGTLIEAEACDVGFREVRI-ENGLLLLNGKPLL 351 Query: 348 INGVNRHEWNAHTGRVISMDDMRADIQTMLANNINADRTCHYPDQLPWYQLCDEAGIYLM 407 I GVNRHE + G+V+ M DI M NN NA R HYP+ WY LCD G+Y++ Sbjct: 352 IRGVNRHEHHPLHGQVMDEQTMVQDILLMKQNNFNAVRCSHYPNHPLWYTLCDRYGLYVV 411 Query: 408 AENNLESHGSWQKMGAIEPSYNVPGDNPHWLAAVIDRARSNYEWFKNHPSIIFWSLGNES 467 E N+E+HG N D+P WL A+ +R + +NHPS+I WSLGNES Sbjct: 412 DEANIETHGM--------VPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSLGNES 463 Query: 468 YAGEDIAAMQAFYKEHDDSRLVHYEGVVHTPELKDRISDVESRMYEKPQ-------NIVA 520 G + A+ + K D SR V YEG D I + +R+ E +I Sbjct: 464 GHGANHDALYRWIKSVDPSRPVQYEGGGADTTATDIICPMYARVDEDQPFPAVPKWSIKK 523 Query: 521 YLE-DNPTKPFLDCEYMHDMGNSLGGMQSYNDLIDKYPMYQGGFIWDFIDQALFVHDPIT 579 +L T+P + CEY H MGNSLGG Y +YP QGGF+WD++DQ+L +D Sbjct: 524 WLSLPGETRPLILCEYAHAMGNSLGGFAKYWQAFRQYPRLQGGFVWDWVDQSLIKYDE-N 582 Query: 580 DQDVLRYGGDFDERHSDYEFSGDGLMFADRTPKPAMQEVKY 620 YGGDF + +D +F +GL+FADRTP PA+ E K+ Sbjct: 583 GNPWSAYGGDFGDTPNDRQFCMNGLVFADRTPHPALTEAKH 623 Lambda K H 0.320 0.138 0.429 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: 1868 Number of extensions: 99 Number of successful extensions: 8 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: 1024 Length adjustment: 41 Effective length of query: 585 Effective length of database: 983 Effective search space: 575055 Effective search space used: 575055 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: 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:
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