Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_000191585.1:WP_013645374.1 Length = 223 Score = 132 bits (331), Expect = 1e-35 Identities = 77/216 (35%), Positives = 124/216 (57%), Gaps = 7/216 (3%) Query: 4 LQLSDVRKSY--GGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLT 61 +++ +++K Y G + + VDL+I+ GE V +GPSG GKSTLL MI GL++ + G ++ Sbjct: 7 IKIKNLKKEYEDGSIIALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDKANEGQIS 66 Query: 62 IDDVRMNDVDP----SKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEA 117 + V + D I VFQ + L P++TV EN+ L + ++E+R + Sbjct: 67 VAGVNLMDNSDLSNFRSNEIGFVFQLHNLIPNLTVLENVQIPLLGTDIDDKKMEERALKL 126 Query: 118 AHILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIA 177 + L +D+KP +LSGG+RQRVAI RA+V HP I L DEP LD+E + + + Sbjct: 127 LKSVNLENKVDQKPTKLSGGERQRVAIARALVNHPSIILADEPTGALDSETQEVILKLLL 186 Query: 178 RLHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVE 213 +HK+ T++ VTH+ A AD+ + + G ++ Sbjct: 187 DIHKKENVTLIMVTHEPYVAKQ-ADRSIYVLDGKIK 221 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: 179 Number of extensions: 10 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: 223 Length adjustment: 26 Effective length of query: 332 Effective length of database: 197 Effective search space: 65404 Effective search space used: 65404 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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