Align LVIS_2259 + LVIS_2258 (EC 3.2.1.23) (characterized)
to candidate 1936924 b3076 cryptic beta-D-galactosidase, alpha subunit (NCBI)
Query= CAZy::ABJ65308.1 (628 letters) >FitnessBrowser__Keio:1936924 Length = 1030 Score = 345 bits (884), Expect = 7e-99 Identities = 212/618 (34%), Positives = 329/618 (53%), Gaps = 51/618 (8%) Query: 17 NQLPAHSDHRGYASVEEATA---QHSSLVQSLDGTWQFAFAPDPVHRFEGFYQPDYDRSA 73 N+L + Y SV +A + SSL L G W F F P+ E F + Sbjct: 13 NRLAPRAYFFSYDSVAQARTFARETSSLFLPLSGQWNFHFFDHPLQVPEAFTSELM--AD 70 Query: 74 FDRLTVPGHIELAGYGQIQYINTAYPWEGHHYRRPAYSMGADQPEKGMFSTDPQNTVGAY 133 + +TVP ++ G+G++QY + +P+ D P N GAY Sbjct: 71 WGHITVPAMWQMEGHGKLQYTDEGFPFP------------IDVP-----FVPSDNPTGAY 113 Query: 134 VKHFTLNPALANQRVSIEFDGVEQAMFLWLNGQFVGYAEDSFSRSEFDLTPYLQAGQNLL 193 + FTL+ ++ I+FDGVE +++NGQ+VG+++ S +EFD++ ++ G NLL Sbjct: 114 QRIFTLSDGWQGKQTLIKFDGVETYFEVYVNGQYVGFSKGSRLTAEFDISAMVKTGDNLL 173 Query: 194 AVEVFKHSTAAFLEDQDMFRFSGIFRSVRLVAKPELHVEDLTIRAGLDDAFQTGDLKVRL 253 V V + + + ++EDQDM+ +GIFR V LV K H+ D T+R D+A+ L + Sbjct: 174 CVRVMQWADSTYVEDQDMWWSAGIFRDVYLVGKHLTHINDFTVRTDFDEAYCDATLSCEV 233 Query: 254 QLTAASQLSGTATAQLLTADGQEVW---ATEQPAASTLDLAA---AIDHVHLWDHHDPYL 307 L + T + DG+ V A + A L A+ ++ W PYL Sbjct: 234 VLENLAASPVVTTLEYTLFDGERVVHSSAIDHLAIEKLTSASFAFTVEQPQQWSAESPYL 293 Query: 308 YQLRITLKDVAGQVVEVVPYPVGFRRIELKDKVMCLNGQRLILNGVNRHEWDAHRGRAVT 367 Y L +TLKD G V+EVVP VGFR I+++D + +N + ++L+GVNRH+ D +GRAV Sbjct: 294 YHLVMTLKDANGNVLEVVPQRVGFRDIKVRDGLFWINNRYVMLHGVNRHDNDHRKGRAVG 353 Query: 368 MADMTQDLQTFHDNHINAVRTCHYPDQDAWYYLCDQQGIYMMAENNLETHGTWQKMGAVE 427 M + +DLQ ++IN+VRT HYP+ +Y LCD G+++MAE ++E+HG + +G + Sbjct: 354 MDRVEKDLQLMKQHNINSVRTAHYPNDPRFYELCDIYGLFVMAETDVESHG-FANVGDIS 412 Query: 428 PSYNVPGSLPQWQLAVLDRAKSNYEMFKNHPAVLFWSLGNESYAGDNIAAMDAFYHHA-- 485 + PQW+ ++R + KNHP+++ WSLGNES G NI AM YH A Sbjct: 413 RITDD----PQWEKVYVERIVRHIHAQKNHPSIIIWSLGNESGYGCNIRAM---YHAAKA 465 Query: 486 -DPTRLTHYEGVCRNRVYEDR---ISDMESMMYDPPRAIEDYLKNDPQKPFVNCEYMHDM 541 D TRL HYE EDR + D+ S MY + ++ + KP + CEY H M Sbjct: 466 LDDTRLVHYE--------EDRDAEVVDIISTMYTRVPLMNEFGEYPHPKPRIICEYAHAM 517 Query: 542 GNSLGGMASYDALIDQYPMYQGGFIWDFIDQALWVKDEVTGQPVLRYGGDFDDRHSDYEF 601 GN GG+ Y + ++ QG ++W++ D + +D+ G ++GGD+ D ++Y F Sbjct: 518 GNGPGGLTEYQNVFYKHDCIQGHYVWEWCDHGIQAQDD-HGNVWYKFGGDYGDYPNNYNF 576 Query: 602 SGDGLLFADRTPKPALQE 619 DGL+++D+TP P L+E Sbjct: 577 CLDGLIYSDQTPGPGLKE 594 Lambda K H 0.320 0.136 0.428 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: 1888 Number of extensions: 103 Number of successful extensions: 7 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: 628 Length of database: 1030 Length adjustment: 41 Effective length of query: 587 Effective length of database: 989 Effective search space: 580543 Effective search space used: 580543 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