Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Synpcc7942_2495 Synpcc7942_2495 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__SynE:Synpcc7942_2495 Length = 313 Score = 175 bits (444), Expect = 1e-48 Identities = 103/315 (32%), Positives = 173/315 (54%), Gaps = 22/315 (6%) Query: 4 FVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIF-- 61 ++Q L+NGL +G +Y L A+GYT+V+ I+G+INFAHG +F LG A + + ++ F Sbjct: 3 WLQPLINGLAIGGVYALFALGYTLVFSILGVINFAHGAVFTLG---AYLTYALVGGRFSF 59 Query: 62 ------AGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPL--RGSFRLAPLITAIGMSI 113 A LP ++ + L++ L+ + IE+VA+RPL R + L LI+++G+++ Sbjct: 60 NGLLANAALPFSLPFALALLLGSLLAGGASLLIEQVAFRPLRRRQADPLLTLISSLGVAV 119 Query: 114 TLSNFIQVTQGPRNKPIPPMV----SSVYQFGN----ISVSLKQIIIIVITAVLLTIFWY 165 + N IQ+ G P + S G+ I + QII+ V+ + ++ + Sbjct: 120 FIVNLIQILVGAEIYTFPSNIYGDLPSAINLGSSDRPIQIRTVQIILFVVAIAMFSLLTW 179 Query: 166 IVNRTALGRAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFN 225 ++N T +G A +A +D A+LLG++ D+ I +TF + L +AGT+ + Sbjct: 180 LINGTRVGHALKAVAEDATTASLLGIDPDRYIRLTFFLSGVLGGLAGTLVGTSVSITGPY 239 Query: 226 DGFTPGVKAFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLI 285 G G+K + VLGG+G++PG + GGLL+GL E+ W Y+D FA+L +L+ Sbjct: 240 FGIAYGLKGLSVMVLGGLGNIPGTIAGGLLLGLAEA-WVPPQWSGYRDAVAFALLFAMLL 298 Query: 286 FKPTGILGRPEVEKV 300 +P G+ R EKV Sbjct: 299 IRPQGLFSRARTEKV 313 Lambda K H 0.329 0.143 0.421 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: 321 Number of extensions: 26 Number of successful extensions: 6 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: 300 Length of database: 313 Length adjustment: 27 Effective length of query: 273 Effective length of database: 286 Effective search space: 78078 Effective search space used: 78078 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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