Align ABC transporter for Lactose, periplasmic substrate-binding component (characterized)
to candidate YP_002822488.1 NGR_b02700 Lactose-binding protein
Query= reanno::Smeli:SM_b21652 (424 letters) >NCBI__GCF_000018545.1:YP_002822488.1 Length = 424 Score = 790 bits (2040), Expect = 0.0 Identities = 384/424 (90%), Positives = 401/424 (94%) Query: 1 MDIQTRAYLPRIAGLALAGASFLGVTAAQAKEITIWCWDPNFNVAIMKEAGARYTKTHPD 60 MD RA+LPRIA LALA AS L VTAA+AKEITIWCWDPNFNVAIMKEAGARYTKTHPD Sbjct: 1 MDNFARAHLPRIAALALASASLLAVTAAEAKEITIWCWDPNFNVAIMKEAGARYTKTHPD 60 Query: 61 VTFNIVDFAKLDVEQKLQTGLSSGTADALPDIVLIEDYGAQKYLQSFPGAFAPLSGTVDY 120 VTFN+VDFAK DVEQKLQTGL+SGTADALPDIVLIEDYGAQKYLQSFPGAFAPLSGTVDY Sbjct: 61 VTFNVVDFAKTDVEQKLQTGLASGTADALPDIVLIEDYGAQKYLQSFPGAFAPLSGTVDY 120 Query: 121 SGFAPYKVELMTLDGQVYGMPFDSGVTGLYYRKDYLEAAGFKPEDMQDLTWDRFIEIGKQ 180 SGFAPYKVE+MT+DGQVYGMPFDSGVTGLYYRKDYLE AGFKPEDMQ+LTWDRFIEIGK+ Sbjct: 121 SGFAPYKVEVMTVDGQVYGMPFDSGVTGLYYRKDYLEQAGFKPEDMQNLTWDRFIEIGKE 180 Query: 181 VEEKTGKKMMGLDPNDAGLVRIIMQSAGQWYFDKEGKPNIAGNAALKAALETIGKIMQAN 240 VE KTGKKMMGLDPND GLVRIIMQSAGQWYFDKEGKPNI GN ALKAA+ET+GKIM AN Sbjct: 181 VEAKTGKKMMGLDPNDGGLVRIIMQSAGQWYFDKEGKPNITGNPALKAAVETVGKIMSAN 240 Query: 241 IYKPANGWSDWVGTFTSGDVATVVTGVWITGTVKAQPDQSGNWGVAPIPALSIEGATHAS 300 IYKPANGWSDWVGTFTSGDVA+VVTGVWITGTVKAQPDQ+G WGVAPIPALSIEGATHAS Sbjct: 241 IYKPANGWSDWVGTFTSGDVASVVTGVWITGTVKAQPDQAGKWGVAPIPALSIEGATHAS 300 Query: 301 NLGGSSWYVLESSEEKAEAIDFLNEIYAKDIDFYQKILQDRGAVGSLLAARGGAAYEAAD 360 NLGGSSWYVLESS EKAEAIDFLNEIY KDIDFYQKILQDRGAVGSLLAARGGAAYEAAD Sbjct: 301 NLGGSSWYVLESSAEKAEAIDFLNEIYGKDIDFYQKILQDRGAVGSLLAARGGAAYEAAD 360 Query: 361 PFFGGEKVWQNFSDWLAKVPSVNYGIFTNEADLAVTAQLPAVTQGTPVDEVLQAIEAEVS 420 PFFGGEKVWQNFSDWL KVPSVNYG+FTNEADLAVTAQLPA+TQG PVD+ L+AIE E+S Sbjct: 361 PFFGGEKVWQNFSDWLVKVPSVNYGVFTNEADLAVTAQLPALTQGMPVDDALKAIETEIS 420 Query: 421 AQIQ 424 IQ Sbjct: 421 GHIQ 424 Lambda K H 0.316 0.134 0.401 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: 713 Number of extensions: 18 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: 424 Length of database: 424 Length adjustment: 32 Effective length of query: 392 Effective length of database: 392 Effective search space: 153664 Effective search space used: 153664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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