Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_012102195.1 CKL_RS08845 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_000016505.1:WP_012102195.1 Length = 352 Score = 206 bits (525), Expect = 6e-58 Identities = 105/262 (40%), Positives = 164/262 (62%), Gaps = 5/262 (1%) Query: 4 LQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID 63 +++ ++ K++G E K + I+ G+ + +GPSG GK+T+LR+IAGLE SG++ ID Sbjct: 3 VEVRNLNKNFGSYEASKNISFGIERGKLIGLLGPSGSGKTTILRIIAGLETADSGEIYID 62 Query: 64 DVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILEL 123 +ND+ P KRGI VFQ+YAL+ +MTV +N+ F L + I++RV E ++ L Sbjct: 63 GKLVNDISPGKRGIGFVFQNYALFRNMTVYQNIAFGLSIKKEDKKYIKERVTELIELIGL 122 Query: 124 GALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQL 183 L R P QLSGGQ+QRVA RAI P++ L DEP + +DA++R +R + ++ +L Sbjct: 123 KGLEKRYPSQLSGGQKQRVAFARAIAPKPQLLLLDEPFAAIDAKVRKELRTWLKQMIHKL 182 Query: 184 ATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLK 243 T V+VTHDQ EA+ +AD+I++ G +EQ+GS +++Y +P FVA F+G + Sbjct: 183 GITSVFVTHDQEEAVEVADEIIITNLGSIEQIGSAVEIYKNPQTAFVATFVGESTI---- 238 Query: 244 GVIEIDEDQAYARLPDYGDAKI 265 + + E +A+ RLP A I Sbjct: 239 -IKDFSEFKAFKRLPSGAKAII 259 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: 297 Number of extensions: 13 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: 358 Length of database: 352 Length adjustment: 29 Effective length of query: 329 Effective length of database: 323 Effective search space: 106267 Effective search space used: 106267 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: 49 (23.5 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