Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_084934899.1 HA51_RS12950 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_002095475.1:WP_084934899.1 Length = 367 Score = 258 bits (658), Expect = 2e-73 Identities = 147/361 (40%), Positives = 213/361 (59%), Gaps = 11/361 (3%) Query: 1 MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60 MS L L + K++G + + D G FV +GPSGCGKSTLLR IAGLE SG++ Sbjct: 1 MSHLSLHHITKAWGEKIALNDISFDAAEGSFVALLGPSGCGKSTLLRTIAGLETADSGEI 60 Query: 61 TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120 + + PS+R ++MVFQSYAL+PH+ VREN+ F L+ G + R+++ + + Sbjct: 61 HFKHSDITHLPPSQRKLSMVFQSYALFPHLNVRENLLFGLKARGEDKQTFTTRLDDVSKL 120 Query: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180 +EL LLDR P QLSGGQ+QRVA+GRA++ + + L DEPLSNLDA+LR MR EI L Sbjct: 121 MELDKLLDRLPSQLSGGQQQRVALGRAVIANNNLCLMDEPLSNLDAKLRQSMRREIRALQ 180 Query: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMN 240 K+LA T++YVTHDQ EAM++AD I+++ G +EQ G+P DLY++PA +F A FIG+P MN Sbjct: 181 KKLALTMLYVTHDQTEAMSMADSIILLNDGHIEQHGTPNDLYNNPATIFAAQFIGAPPMN 240 Query: 241 FLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHFD--EAGPAALDLAI 298 L + +Q Y + PV ++ A+++G+R E A AAL + Sbjct: 241 ILP--LHAKGEQHY-----LSHLQTPV-VERCDEVALSLGLRAEDIQLISADNAALTARV 292 Query: 299 DMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDG-EGKRLR 357 E++G +T + G EL+ V+ + G + ++ +F GKR Sbjct: 293 ISYEYMGSDTLLACQLAGLSELVTVKVPGMQRYDEGSLVGLQWSAARQYLFSSTSGKRCA 352 Query: 358 S 358 S Sbjct: 353 S 353 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: 282 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: 367 Length adjustment: 29 Effective length of query: 329 Effective length of database: 338 Effective search space: 111202 Effective search space used: 111202 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