Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_011384263.1 AMB_RS09395 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_000009985.1:WP_011384263.1 Length = 273 Score = 157 bits (396), Expect = 4e-43 Identities = 84/198 (42%), Positives = 114/198 (57%), Gaps = 3/198 (1%) Query: 12 SYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDDVRMNDVD 71 S+G ++ L+I+ GEFV +GPSGCGKST L +AG + G + +D V + Sbjct: 25 SFGAHAAVEDFSLEIEPGEFVCLLGPSGCGKSTALNAVAGFLRPARGRVAVDGVEVTGPG 84 Query: 72 PSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGALLDRKP 131 P + MVFQ ++L+P TV EN+ F R G RAE E ++ LG R P Sbjct: 85 PER---GMVFQQHSLFPWKTVLENVAFGPRMQGKTRAEARDLAREYLDLVGLGGSAQRYP 141 Query: 132 KQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLATTIVYVT 191 LSGG QRV I RA+V HP + L DEP LDA+ R M+ + RL Q+ T+++VT Sbjct: 142 AALSGGMAQRVGIARALVNHPSVLLMDEPFGALDAQTRSIMQESLLRLWGQIGNTVLFVT 201 Query: 192 HDQVEAMTLADKIVVMRA 209 HD EA+ LAD++VVM A Sbjct: 202 HDIDEALFLADRVVVMSA 219 Lambda K H 0.321 0.139 0.396 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: 232 Number of extensions: 8 Number of successful extensions: 2 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: 358 Length of database: 273 Length adjustment: 27 Effective length of query: 331 Effective length of database: 246 Effective search space: 81426 Effective search space used: 81426 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: 48 (23.1 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