Align LacG, component of Lactose porter (characterized)
to candidate AZOBR_RS00065 AZOBR_RS00065 glycerol-3-phosphate transporter membrane protein
Query= TCDB::P29824 (273 letters) >FitnessBrowser__azobra:AZOBR_RS00065 Length = 276 Score = 156 bits (395), Expect = 4e-43 Identities = 89/275 (32%), Positives = 151/275 (54%), Gaps = 12/275 (4%) Query: 11 DIVQYSVLSLAAFLSIFPFIWMVIGTTNTTSQIIRGKV--TFGTALFDNIASFFAQ---- 64 DIV + +L L + FP +IG+T + I RG + T G + +N AS +++ Sbjct: 2 DIVPHLILMLGVLIFAFPIYVTIIGSTWDAATIGRGNLPLTPGGEMLNNYASAWSESQGN 61 Query: 65 ----VDVPLVFWNSVKIALVGTALTLLVSSLAGYGFEMFRSKLRERVYTVILLTLMVPFA 120 V ++ WNS+ +ALV + +S ++ Y FR LR + +I +TLM+P Sbjct: 62 RVMHTPVRIMMWNSLVMALVIALGKIAISIISAYAVAFFRFPLRMVFFWMIFITLMLPVE 121 Query: 121 ALMIPLFMLMGQAGLLNTHIAIMLPMIASAFIIFYFRQASKAFPTELRDAAKVDGLKEWQ 180 +IP + ++ GL++++ + +P+IASA FRQ P EL +AAK+DG + Sbjct: 122 VRIIPTYEVVANLGLIDSYAGLTIPLIASATATLLFRQFFLTIPDELVEAAKIDGAGALR 181 Query: 181 IFFYIYVPVMRSTYAAAFVIVFMLNWNNYLWPLIVLQSNDTKTITLVVSSLA--SAYSPE 238 F + +P+ R+ AA FVI+F+ WN YLWPL++ S + +T+ + ++ + + + Sbjct: 182 FFLDVVLPLSRTNIAALFVILFIYGWNQYLWPLLITNSAEMETVVIGITKMIGNGEAATD 241 Query: 239 YGTVMIGTILATLPTLLVFFAMQRQFVQGMLGSVK 273 + +M T+LA LP + V MQR FV+G++ S K Sbjct: 242 WNLIMATTVLAMLPPVAVVVLMQRWFVKGLVDSEK 276 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: 275 Number of extensions: 19 Number of successful extensions: 3 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