Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate CCNA_00294 CCNA_00294 phosphate transport ATP-binding protein pstB
Query= reanno::Smeli:SMc02121 (258 letters) >FitnessBrowser__Caulo:CCNA_00294 Length = 274 Score = 137 bits (346), Expect = 2e-37 Identities = 94/263 (35%), Positives = 140/263 (53%), Gaps = 19/263 (7%) Query: 4 TATAPKLAVSTTDVAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRC 63 T+TA A +T D I+ + +YGD L D++L + GPSG GKST +RC Sbjct: 15 TSTA---APATADPKIKARGVKVFYGDKQALFDVDLDIPAKSVTAFIGPSGCGKSTFLRC 71 Query: 64 INRLEE-----HQKGKIVVDGIELTNDLKKIDEV--RREVGMVFQHFNLFPHLTILENCT 116 INR+ + +G I++DG ++ + K +D V R VGMVFQ N FP TI EN Sbjct: 72 INRMNDTIPSARVEGSILIDGADV--NAKSVDPVVLRSRVGMVFQKPNPFPK-TIFENVA 128 Query: 117 LAP-IWVRKMPKKEAEQVAMHFLERVKIPEQA---LKYPGQ-LSGGQQQRVAIARSLCMR 171 P I K E E + L++ + + L PG LSGGQQQR+ IAR++ + Sbjct: 129 YGPRIHGLATGKAELEAIVESSLKKAGLWNEVADRLHQPGTGLSGGQQQRLVIARAIAVS 188 Query: 172 PKILLFDEPTSALDPEMVKEVLDTMVGLAEEGMTMICVTHEMGFARQVANRVIFMDQGQI 231 P+++L DEP SALDP + ++ ++ ++ VTH M A +V+ R F G++ Sbjct: 189 PEVILMDEPCSALDP-IATAKIEELIDELRSQFCIVIVTHSMAQAARVSQRTAFFHLGKL 247 Query: 232 VEQNSPAEFFDNPQHERTKLFLS 254 VE E F NP+ RT+ +++ Sbjct: 248 VESGPTEEMFTNPRDSRTQDYIT 270 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: 151 Number of extensions: 9 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: 274 Length adjustment: 25 Effective length of query: 233 Effective length of database: 249 Effective search space: 58017 Effective search space used: 58017 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 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