Align β-galactosidase (β-gal;BgaA) (EC 3.2.1.23) (characterized)
to candidate WP_005455440.1 SACCYDRAFT_RS08615 glycoside hydrolase family 2
Query= CAZy::ABW87309.1 (574 letters) >NCBI__GCF_000244975.1:WP_005455440.1 Length = 848 Score = 246 bits (628), Expect = 3e-69 Identities = 203/592 (34%), Positives = 263/592 (44%), Gaps = 77/592 (13%) Query: 5 PNHPRPTLQRPGWRSLEGHWDFA--LSEAEAPGGVRFDRKILVPFPPEAPGSGVGEAWVG 62 P +PRP L RP WR+L G W+FA E P G +ILVP+P E+ SG+ + Sbjct: 69 PEYPRPQLTRPEWRNLNGVWEFAGATEGEEPPFGETLPERILVPYPTESALSGI-QRHED 127 Query: 63 VAWYRKVLRAKPRPGR-----RLFLRFGAVDYRAEVFVNGVRVLEHEGGHTPFGLDLTPF 117 WYR+ PR R RL L FGAVDY A V+VNG V H GG+ F D+T Sbjct: 128 HMWYRRTFDV-PRKWRIGEHNRLVLHFGAVDYEATVYVNGREVASHTGGYGAFSADVTDA 186 Query: 118 LER--PVEVLVRAEDDPLDPEAPRGKQALGEPGGIFYPRTTGIWQPVWLEWVPESHIAAL 175 L+ E++V D P GKQ GIFY +GIWQ VWLE V +H+ L Sbjct: 187 LKPHGEQEIVVGVTDRTDATWQPVGKQRRVPDRGIFYEGASGIWQTVWLEPVASAHVTTL 246 Query: 176 RLTPDLKALGFHLEVQAQGEGEAVEVALFPGVRGEAPLGKAPWLEARFPLLGGRASGFLG 235 + PD+ +L V G E V EA + + +R G A L Sbjct: 247 DMVPDIDTSTLNLTVNTVGASERTTV--------EAVVRDGRRVVSR---TRGDADEPLS 295 Query: 236 LPARGNPEGLLWRPETPVLFPLRLRLLSGR---RVLDEVYSYGGLREVAAQRGV-----F 287 LP P LW P++P L+ L + L G R +D V SY G+RE+ G Sbjct: 296 LPV---PNAKLWSPDSPFLYDLDVVLRDGDGRGRPVDRVSSYFGMREIGMAEGEDGRLRI 352 Query: 288 LLNGEPYFPRLVLDQGLWPEGHLAPPGLAALRRDAALAKALGFNGVRKHQKVEDPRYLHL 347 LNGE F LDQG WP+G P ALR D K LGFN VRKH K E R+ + Sbjct: 353 TLNGEILFLMSTLDQGYWPDGIYTAPTDEALRWDLEAHKRLGFNTVRKHIKTEPDRWYYH 412 Query: 348 ADRLGLLVFAEMPSF---FRFSPKAARRYLAELAEALERDRNHPSLVAWILFNEGWGLTP 404 ADRLGLLV+ +MPS R AA ++ AEL E +E +N S++ W+ FNEGWG Sbjct: 413 ADRLGLLVWQDMPSMRTGGRPPADAAAQFEAELHELVEEKKNWTSIIGWVPFNEGWG--E 470 Query: 405 WRAETLAFLQGAFLLARALDPTRPLVDNDGFE------HGPFWDLLTVHDYAPPEVLARR 458 W E + DPTR + + G ++ H Y P Sbjct: 471 WSREATGRIAEE---VAEQDPTRLVNAHSGVNCCDSLGDSGKGHVIDWHAYVGPAT---- 523 Query: 459 YGEGLPEAPMGRPLALAGLPPGVRPFLSEFGGLRLKGPGPGW-----GYREAEDEE---- 509 P +++ G E GG L+ G W Y+ D E Sbjct: 524 ------PTPDEHRVSIDG----------EHGGFGLEVDGHMWFGEGHAYQMLPDSESLTA 567 Query: 510 AFLREVLRYLETACGSRLSGFCYTQLYDTFQEENGLLDFWRR-PKVPPERVR 560 A++ L A +SG YTQ+ D E NG + R+ K+ E VR Sbjct: 568 AYVDNQRAVLHAARSCGISGAIYTQITDVEHEVNGFFTYDRQVEKMDFEAVR 619 Lambda K H 0.322 0.144 0.467 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: 1521 Number of extensions: 89 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 574 Length of database: 848 Length adjustment: 39 Effective length of query: 535 Effective length of database: 809 Effective search space: 432815 Effective search space used: 432815 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 (21.9 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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