Align β-galactosidase (β-gal;BgaA) (EC 3.2.1.23) (characterized)
to candidate WP_005458420.1 SACCYDRAFT_RS18170 glycoside hydrolase family 2
Query= CAZy::ABW87309.1 (574 letters) >NCBI__GCF_000244975.1:WP_005458420.1 Length = 586 Score = 269 bits (687), Expect = 3e-76 Identities = 216/583 (37%), Positives = 268/583 (45%), Gaps = 83/583 (14%) Query: 5 PNHPRPTLQRPGWRSLEGHWDFALSEAEAPGGVRFDRKILVPFPPEAPGSGVGEAWVGVA 64 P HPRP L RP WR+L G WD+ + G V +ILVP+PPE+ S +G + Sbjct: 28 PEHPRPQLTRPNWRTLNGLWDYVGQDEN--GAVHRGERILVPYPPESRLSRIGRRDERM- 84 Query: 65 WYRKVLRAKP--RPGRRLFLRFGAVDYRAEVFVNGVRVLEHEGGHTPFGLDLTPFL--ER 120 WY + P R GR L L FGAVD A V+VN + HEGG+T F +D+T L + Sbjct: 85 WYHRTFDVPPEWRVGRVL-LHFGAVDQTATVWVNHQPLARHEGGYTAFTVDITDVLRPDA 143 Query: 121 PVEVLVRAEDDPLDPEAPRGKQALGEPGGIFYPRTTGIWQPVWLEWVPESHIAALRLTPD 180 EVLVRA+D+ GKQA PGGI Y +GIWQ VWLE VP H+ L + PD Sbjct: 144 EQEVLVRADDEGNRGTFAVGKQA-NRPGGILYTGCSGIWQTVWLEAVPAVHVTELDMEPD 202 Query: 181 LKALGFHLEVQAQGEGEAVEVALFPGVRGEAPLGKAPWLEARFPLLGGRASGFLGLPARG 240 L GF L G V V++ G + A G L L Sbjct: 203 LH--GFDLVAHVAGAHGKVAVSVEVSAAGGEQVASAR----------GNPGERLRLDV-- 248 Query: 241 NPEGLLWRPETPVLFPLRLRLLSGR-RVLDEVYSYGGLREVAAQ------RGVFLLNGEP 293 P+ LLW P+ P L+ + +R++ VLDEV SY LR V R V LLN P Sbjct: 249 -PDPLLWSPDHPHLYDVTVRVVGDDGAVLDEVASYTALRTVRVDTEGDGPRRV-LLNDRP 306 Query: 294 YFPRLVLDQGLWPEGHLAPPGLAALRRDAALAKALGFNGVRKHQKVEDPRYLHLADRLGL 353 F LDQG WP+G P ALR D KALGFN VRKH KVE R+ H AD+LGL Sbjct: 307 VFLNAPLDQGYWPDGIYTAPTDEALRFDLERIKALGFNSVRKHVKVEPMRWYHWADKLGL 366 Query: 354 LVFAEMPSF--FRFSPK---------AARRYLAELAEALERDRNHPSLVAWILFNEGWGL 402 LV+ +MPS +P A R+ EL L + RN PS+V W++FNEGWG Sbjct: 367 LVWQDMPSLPVVLDNPPGPQQPPVVVARERFETELRAMLHQLRNVPSIVVWVVFNEGWG- 425 Query: 403 TPWRAETLAFLQGAFLLARALDPTRPLVDNDGFE------HGPFWDLLTVHDYAPPEVLA 456 +T + +A DP R +V G D+ H Y Sbjct: 426 ---EYDTARITEE----VKATDPGRLVVAASGVNCCHSHPDSGAGDVYDDHTYV------ 472 Query: 457 RRYGEGLPEAPMGRPLALAGLPPGVRPFLSEFGGLRL-----KGPGPGWGYREAEDEEAF 511 G G PE P A+ EFGG+ L PG Y D + Sbjct: 473 ---GPGRPELAATDPRAIVD---------GEFGGVGLVVEGHLWPGEPMAYEMVSDRDRL 520 Query: 512 LR---EVLRYLETACGSRLSGFCYTQLYDTFQEENGLLDFWRR 551 E+ LE RLSG YTQ+ D E NGLL + RR Sbjct: 521 TERYVELSTELEALARDRLSGAVYTQITDVENEVNGLLTYDRR 563 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: 1080 Number of extensions: 68 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: 574 Length of database: 586 Length adjustment: 36 Effective length of query: 538 Effective length of database: 550 Effective search space: 295900 Effective search space used: 295900 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: 53 (25.0 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