Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 8500740 DvMF_1483 inner-membrane translocator (RefSeq)
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__Miya:8500740 Length = 295 Score = 156 bits (394), Expect = 6e-43 Identities = 94/289 (32%), Positives = 152/289 (52%), Gaps = 11/289 (3%) Query: 6 QQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLP 65 Q L+GLT GS+Y L+A+GY++++ G++NF GD LGG L+++ +L S GLP Sbjct: 11 QYTLSGLTTGSVYALLALGYSLIFNATGIVNFTQGDFLSLGG---LVLYSLLVS--QGLP 65 Query: 66 VAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQGP 125 + ++V L +L +ERV RP R + + + S + ++ G Sbjct: 66 IVAAFPATILVVALAGAL----VERVCLRPARSRQMIILIFITMAASTLMRGLMKEGWGK 121 Query: 126 RNKPIPPMVSSV-YQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQDRK 184 +PP+ V ++ ++ + + ++ +T + + T G+A RA D + Sbjct: 122 LPLALPPLSPEVPFRLLGAVLTPQNLWVMGMTLCGIAALAWFFRATVTGKAMRAAAADPR 181 Query: 185 MAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVLGGIG 244 A L+GV V++ +++F AL A+ G M + S++ G G+K F AAVLGG G Sbjct: 182 TARLMGVEVERLTTLSFAFAGALGALGG-MLITPITSLSYDIGLMLGLKGFAAAVLGGYG 240 Query: 245 SLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILG 293 S GAV GG+L+GL ES + Y T AY+DV F +L VL +P G+ G Sbjct: 241 SFAGAVAGGVLLGLFESYGAGYVTSAYRDVLVFGLLILVLFVRPQGLFG 289 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: 293 Number of extensions: 18 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: 300 Length of database: 295 Length adjustment: 26 Effective length of query: 274 Effective length of database: 269 Effective search space: 73706 Effective search space used: 73706 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