Align LacG, component of Lactose porter (characterized)
to candidate Synpcc7942_0471 Synpcc7942_0471 ABC-type sugar transport system permease component-like
Query= TCDB::P29824 (273 letters) >FitnessBrowser__SynE:Synpcc7942_0471 Length = 276 Score = 152 bits (385), Expect = 6e-42 Identities = 83/263 (31%), Positives = 143/263 (54%), Gaps = 3/263 (1%) Query: 12 IVQYSVLSLAAFLSIFPFIWMVIGTTNTTSQ-IIRGKVTF--GTALFDNIASFFAQVDVP 68 ++ Y +L A + P +W+V + + I + F DN + + + Sbjct: 10 LLLYLLLGTIAVAMLIPLLWLVSTAFKSAGEDIFQFPPQFLPTQPTLDNFRRVWTENPLG 69 Query: 69 LVFWNSVKIALVGTALTLLVSSLAGYGFEMFRSKLRERVYTVILLTLMVPFAALMIPLFM 128 F NS +AL+ L LL SLA Y K R+ ++ +I+ T+++PF +MIPL++ Sbjct: 70 QYFLNSTWVALLTVGLNLLFCSLAAYPLARLEFKGRQTLFLLIVATILIPFQVVMIPLYV 129 Query: 129 LMGQAGLLNTHIAIMLPMIASAFIIFYFRQASKAFPTELRDAAKVDGLKEWQIFFYIYVP 188 L+ GL NT++ ++ P +ASAF IF RQA + P +L +AA++DG + +++ + +P Sbjct: 130 LIINLGLRNTYLGLVFPYLASAFGIFLLRQAFQGIPKDLEEAARIDGCNDLGVWWNVMIP 189 Query: 189 VMRSTYAAAFVIVFMLNWNNYLWPLIVLQSNDTKTITLVVSSLASAYSPEYGTVMIGTIL 248 R + VF+ +W+++LWPLI+L D T+ L +++LAS +S ++ V G++L Sbjct: 190 SARPALITLAIFVFIGSWSDFLWPLIILDEPDRYTLPLGIATLASGFSLDWRLVAAGSVL 249 Query: 249 ATLPTLLVFFAMQRQFVQGMLGS 271 + LP VF A+QR V S Sbjct: 250 SILPVFGVFLALQRYIVPSAAAS 272 Lambda K H 0.331 0.140 0.416 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: 244 Number of extensions: 10 Number of successful extensions: 1 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: 273 Length of database: 276 Length adjustment: 25 Effective length of query: 248 Effective length of database: 251 Effective search space: 62248 Effective search space used: 62248 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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