Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate Ac3H11_3200 Amino acid ABC transporter permease protein
Query= reanno::Smeli:SMc02121 (258 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3200 Length = 604 Score = 252 bits (644), Expect = 1e-71 Identities = 130/249 (52%), Positives = 176/249 (70%), Gaps = 10/249 (4%) Query: 19 IEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVVD 78 + I ++K YG VL+D+ L V+ G V+ GPSGSGKST++R IN LE G I +D Sbjct: 356 VTIHGVSKRYGALEVLKDVTLTVLPGSVTVILGPSGSGKSTLLRSINHLERVDGGFIAID 415 Query: 79 G--------IELTNDLKKIDEVRR--EVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKK 128 G + +L + D ++R +VGMVFQ+FNLFPHLT+LEN AP+ VRK+ + Sbjct: 416 GELIGYRQDADALYELGENDILKRRVDVGMVFQNFNLFPHLTVLENIVEAPVTVRKLARA 475 Query: 129 EAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEM 188 EAE +A+ L RV + ++A YP QLSGGQQQRVAIAR+L ++PK+LLFDEPTSALDPE+ Sbjct: 476 EAEALALELLARVGLSDKAHSYPRQLSGGQQQRVAIARALALKPKVLLFDEPTSALDPEL 535 Query: 189 VKEVLDTMVGLAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHER 248 V EVLD + LA G T++ VTHE+GFAR+VA+ V+FM+QG++VE +PA+ F P H R Sbjct: 536 VGEVLDVIKELARTGTTLVIVTHEIGFAREVADTVVFMEQGRVVETGTPAKVFSQPDHPR 595 Query: 249 TKLFLSQIL 257 T FL+++L Sbjct: 596 TAAFLAKVL 604 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: 326 Number of extensions: 8 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: 258 Length of database: 604 Length adjustment: 31 Effective length of query: 227 Effective length of database: 573 Effective search space: 130071 Effective search space used: 130071 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: 50 (23.9 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