Align β-galactosidase (Bga;NixL;XCC2895) (EC 3.2.1.23) (characterized)
to candidate WP_012405729.1 BPHY_RS32570 beta-galactosidase
Query= CAZy::AAM42167.1 (613 letters) >NCBI__GCF_000020045.1:WP_012405729.1 Length = 632 Score = 410 bits (1053), Expect = e-118 Identities = 234/608 (38%), Positives = 339/608 (55%), Gaps = 47/608 (7%) Query: 31 TFATQGTQFVRDGKPYQVLSGAIHFQRIPRTYWKDRLQKARALGLNTVETYVFWNLVEPQ 90 +FA G F+ DGKP+Q+ SG +H RIP YW+ R+Q A+A+G+NT+ YV WN E + Sbjct: 24 SFAPNGDGFLLDGKPFQIRSGELHPARIPVEYWRHRIQMAKAMGMNTIALYVMWNYHETR 83 Query: 91 QGQFDFNANN-DVAAFVREAAAQGLNVILRPGPYACAEWEAGGYPAWLFGKDNIRIR--- 146 +G FDF +N D+ AF+R A+ + V+ RPGPY CAEW+ GG P++L +IR+R Sbjct: 84 EGTFDFQTDNRDIEAFIRLCQAENMWVLFRPGPYVCAEWDLGGIPSYLLKYADIRLRTDY 143 Query: 147 SRDPRFLAASQSYLDAVAQQVRPLLNHNGGPIIAVQVENEYGSYDDDHAYMADNRAMFVK 206 + D R++ A + Y+D + +VRPL+ +GGPI+ +Q+ENE+GS+D + AY+ + R ++++ Sbjct: 144 ASDARYMRAVERYIDELVPRVRPLMAQDGGPILMIQIENEFGSFDRNRAYLEELRQLWMR 203 Query: 207 AGFDKALLFTSDGADMLANG---TLPGTLAVVNFAPGEAKSAFDKLIKFQPDQPRMVGEY 263 G +T DG L G +A+ N + D + K P P M GE Sbjct: 204 GGI-PGPFYTEDGVVQLQQNLSYVADGAIALSNANAAQ----IDAVRKIFPSVPAMAGEV 258 Query: 264 WAGWFDHWGTPHASTNAKQQTEELEWILRQGHSANLYMFIGGTSFGFMNGANFQGNPSDH 323 + GW HWG + + L+ ++R S NLY+ GGTSFGF GAN + S Sbjct: 259 YPGWLTHWGDDAFQGTSVDLSATLDELMRNKQSFNLYVIHGGTSFGFYAGANVDAD-SGE 317 Query: 324 YAPQTTSYDYDAILDEAGRPTPKFALMRDVITRVTGVQPPALPAPIAMAALKDA------ 377 Y P TSYDY A ++E G T ++ R +I R P +P PIA D+ Sbjct: 318 YQPDITSYDYAAPINEQGAATARYLTYRGIIARYLSAPLPDVPMPIATIPSMDSNGIRRL 377 Query: 378 PLRESASLWDNLPAPIA-IDT--PQPMEHFGQDYGYILYRTTVTGPRKESLYLGEVRDVA 434 R ASLWDNLPA +A DT PQP E +GQ +G++LYRT + L +G+V D A Sbjct: 378 MPRRFASLWDNLPAALAPADTMQPQPFEMYGQAFGFVLYRTKLERYAGGMLDIGDVHDYA 437 Query: 435 RVYVDQKPVGSVERR--LQQVATEVDI--------------PAGQHTLDVLVENSGRINY 478 V+V + G+V R +Q+A+ ++ P L++LVE GR+NY Sbjct: 438 TVFVGDQYAGAVSRTRIREQLASPRNVVHRQPVALPDASSAPRASVLLEILVEGMGRVNY 497 Query: 479 GPRMADGRAGLVDPVLLDNQQLTN-----WQAFPLPMRSP--DSIRGWTRNTVEGPAFHR 531 G M D R G+VDPV++ + + W+ PLPM + +++R + F Sbjct: 498 GHSMID-RKGIVDPVVIHDASGASEIPQGWEVVPLPMETSFIENLRPICSDASRPGIFFV 556 Query: 532 GNLRIGTPADTYLDMRAFGKGIAWANGVNLGRHWNIGPQRALYFPAPFQRKGDNTVVVFD 591 L I D YLDM + KGI W NG NLGR+W++GPQ+ LY PAP+ + GDNT+++FD Sbjct: 557 ATLSIRATGDVYLDMSEWIKGIVWVNGRNLGRYWHVGPQKRLYCPAPWLKPGDNTLLIFD 616 Query: 592 LDST-AKP 598 L T AKP Sbjct: 617 LHQTDAKP 624 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: 1131 Number of extensions: 67 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: 613 Length of database: 632 Length adjustment: 37 Effective length of query: 576 Effective length of database: 595 Effective search space: 342720 Effective search space used: 342720 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: 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