Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)
Query= reanno::Smeli:SMc02121 (258 letters) >FitnessBrowser__MR1:200449 Length = 378 Score = 155 bits (393), Expect = 9e-43 Identities = 88/259 (33%), Positives = 144/259 (55%), Gaps = 8/259 (3%) Query: 1 MANTATAPKLAVSTTD--VAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKS 58 MA+T+ + T V ++I ++K + D + D++L + +GE + G SGSGKS Sbjct: 1 MASTSGVTNKPTTKTQEKVLLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKS 60 Query: 59 TMIRCINRLEEHQKGKIVVDGIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLA 118 T++R + E G+I +DG ++T+ + R + M+FQ + LFPH+T+ +N Sbjct: 61 TLLRMLAGFERPTSGRIYLDGEDITD----LPPYERPINMMFQSYALFPHMTVAQNIAFG 116 Query: 119 PIWVRKMPKKEAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFD 178 + K+PK E EQ L+ V + + + P QLSGGQ+QRVA+ARSL RPK+LL D Sbjct: 117 -LKQDKLPKAEIEQRVQEMLKLVHMEQYGKRKPHQLSGGQRQRVALARSLAKRPKLLLLD 175 Query: 179 EPTSALDPEMVKEV-LDTMVGLAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSP 237 EP ALD ++ ++ L+ + L G+T + VTH+ A +A R+ M G I + SP Sbjct: 176 EPMGALDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRISIMSDGWIAQTGSP 235 Query: 238 AEFFDNPQHERTKLFLSQI 256 + +++P F+ + Sbjct: 236 MDIYESPNSRMIAEFIGSV 254 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: 230 Number of extensions: 15 Number of successful extensions: 4 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: 378 Length adjustment: 27 Effective length of query: 231 Effective length of database: 351 Effective search space: 81081 Effective search space used: 81081 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: 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