Align β-galactosidase (Bga;NixL;XCC2895) (EC 3.2.1.23) (characterized)
to candidate CA265_RS06080 CA265_RS06080 beta-galactosidase
Query= CAZy::AAM42167.1 (613 letters) >FitnessBrowser__Pedo557:CA265_RS06080 Length = 611 Score = 483 bits (1243), Expect = e-140 Identities = 251/604 (41%), Positives = 365/604 (60%), Gaps = 10/604 (1%) Query: 15 IALPITATAASDDQWPTFATQGTQFVRDGKPYQVLSGAIHFQRIPRTYWKDRLQKARALG 74 +A+ + TA TF + F+ D KP+Q++SG +H+ R+P+ W+ R++ A+A+G Sbjct: 9 VAMCFSLTAFGQQAKHTFKLGESDFLLDDKPFQIISGELHYPRVPKEAWRARMKMAKAMG 68 Query: 75 LNTVETYVFWNLVEPQQGQFDFNANNDVAAFVREAAAQGLNVILRPGPYACAEWEAGGYP 134 LNT+ TYVFWNL EPQ+G+FDF+ NN++A FV+ A +GL VILRP PY CAEWE GGYP Sbjct: 69 LNTIGTYVFWNLHEPQKGKFDFSGNNNIAEFVKIAQQEGLWVILRPSPYVCAEWEFGGYP 128 Query: 135 AWLFGKDNIRIRSRDPRFLAASQSYLDAVAQQVRPLLNHNGGPIIAVQVENEYGSYDDDH 194 WL + + +RS + ++L + Y+ V +Q+ L ++GG II VQVENEYGSY D Sbjct: 129 YWLQNEKGLVVRSTEKQYLDEYKKYILEVGKQLASLQINHGGNIIMVQVENEYGSYAADK 188 Query: 195 AYMADNRAMFVKAGFDKALLFTSDGADMLANGTLPGTLAVVNFAPGEAKSAFDKLIKFQP 254 Y+ NR MF++AGFD LL+T D A + +G L G L VN AK +L+ Sbjct: 189 NYLDINRKMFIEAGFD-GLLYTCDPAADVKDGHLAGLLPAVNGIDDPAK--IRQLVNENH 245 Query: 255 D--QPRMVGEYWAGWFDHWGTPHASTNAKQQTEELEWILRQGHSANLYMFIGGTSFGFMN 312 D P + E++ WFD WGT H + A Q T+ L+ +L G S N+YMF GGT+ GFMN Sbjct: 246 DGKGPYFIAEWYPAWFDWWGTAHHTVPAVQYTKRLDSVLAAGISINMYMFHGGTTRGFMN 305 Query: 313 GANFQGNPSDHYAPQTTSYDYDAILDEAGRPTPKFALMRDVITR--VTGVQPPALPAPIA 370 GAN++ Y PQT+SYDYDA L+EAG T KF R VI + G P +PA Sbjct: 306 GANYK--DISPYEPQTSSYDYDAPLNEAGNVTEKFRAFRSVIEKHLPAGQSLPPIPAAKP 363 Query: 371 MAALKDAPLRESASLWDNLPAPIAIDTPQPMEHFGQDYGYILYRTTVTGPRKESLYLGEV 430 A+ L +L++ LP + TP E QDYGY+LYRTT+ G +K L L ++ Sbjct: 364 SIAIAPFKLTSKVTLFNALPKAVKNITPLTFEDLKQDYGYVLYRTTIQGGKKGQLQLKQL 423 Query: 431 RDVARVYVDQKPVGSVERRLQQVATEVDIPAGQHTLDVLVENSGRINYGPRMADGRAGLV 490 RD A ++++QK G ++RRL Q +D+PAG+ LD+ VEN GR+N+G + + + G+ Sbjct: 424 RDYALIFINQKRAGILDRRLNQNTLSLDLPAGEVQLDIFVENMGRVNFGKYLLENKKGIT 483 Query: 491 DPVLLDNQQLTNWQAFPLPMRSPD-SIRGWTRNTVEGPAFHRGNLRIGTPADTYLDMRAF 549 + V + ++ NW + P + +I +++ GP +G+ +I T ADTYLDM + Sbjct: 484 EQVTFNGAEVKNWSMYGFPFNNDRMTITSPSKSNGNGPTLQKGSFQIATVADTYLDMTDW 543 Query: 550 GKGIAWANGVNLGRHWNIGPQRALYFPAPFQRKGDNTVVVFDLDSTAKPSVRGLQQQVWI 609 GKG+ W NG NLG++W IGPQ+ LY P + +KG N + V +L + ++ + Q + Sbjct: 544 GKGVVWVNGHNLGKYWAIGPQQTLYVPQEWLKKGKNDITVLELLKPDQNILKAIDQPILN 603 Query: 610 TPKE 613 T K+ Sbjct: 604 TLKK 607 Lambda K H 0.319 0.136 0.425 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: 1073 Number of extensions: 51 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: 613 Length of database: 611 Length adjustment: 37 Effective length of query: 576 Effective length of database: 574 Effective search space: 330624 Effective search space used: 330624 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: 53 (25.0 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