Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc02121 (258 letters) >NCBI__GCF_000230695.2:WP_015448118.1 Length = 255 Score = 132 bits (333), Expect = 5e-36 Identities = 86/239 (35%), Positives = 125/239 (52%), Gaps = 11/239 (4%) Query: 11 AVSTTDVAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEH 70 A S +A + K YG L ++L G + G SGSGKST++R + LE Sbjct: 4 AESAGGIAFALVQAGKRYGRLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWP 63 Query: 71 QKGKIVVDGIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPI---WVRKMPK 127 G + VDG L + +RR VG V Q LFPHLT L N L P W R+ + Sbjct: 64 DHGHVEVDGRPLQRS--DVLPLRRRVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIR 121 Query: 128 KEAEQVAMHFLERVKIPEQAL-KYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDP 186 + AEQ+A +P L +YP +LSGGQ+QRVA+ R+L P LL DEP ALDP Sbjct: 122 QRAEQLAA----LTHLPTGVLERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDP 177 Query: 187 EMVKEVLDTMVGLAEE-GMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNP 244 + E+ D + + ++ G T+I VTH++ A A R++ + QG +++ + + + P Sbjct: 178 VVRHELQDELKQIFDQLGKTVIVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERP 236 Lambda K H 0.322 0.136 0.397 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: 130 Number of extensions: 7 Number of successful extensions: 3 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: 258 Length of database: 255 Length adjustment: 24 Effective length of query: 234 Effective length of database: 231 Effective search space: 54054 Effective search space used: 54054 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 (21.9 bits) S2: 47 (22.7 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