Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 8500415 DvMF_1165 inner-membrane translocator (RefSeq)
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__Miya:8500415 Length = 306 Score = 211 bits (538), Expect = 1e-59 Identities = 119/306 (38%), Positives = 178/306 (58%), Gaps = 6/306 (1%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 ME F+Q L N L GS Y L+A+GYT+VYG++ +INFAHGDIFM+G + A V +L Sbjct: 1 MEIFIQNLFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYIAFFVSSLLLGD 60 Query: 61 FAG---LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLR--GSFRLAPLITAIGMSITL 115 G LP L + + + ML+T+ T+ER+AYRPLR G+ RL +ITA+ + L Sbjct: 61 LLGVFNLPGWAALALTVPLTMLLTAGVGVTLERIAYRPLRRKGAHRLYVVITALMCGLIL 120 Query: 116 SNFIQVTQGPRNKPIPPMVSSV-YQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGR 174 N G + +P MV V Y FG++SV+ ++ +I+ ++ + +IV RT +G Sbjct: 121 ENGNLALLGASRRKLPDMVDKVVYTFGSVSVTNLKVWVIITAFLVFFLLQFIVTRTRIGM 180 Query: 175 AQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKA 234 A RA D+ L+G+ +D I TFV+G+ A +AG ++ M Y + G G KA Sbjct: 181 AMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGWKA 240 Query: 235 FTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGR 294 F AAV+GGIG + GA GG L+ IE + +A+ ++D+ F IL +L +PTG+ G Sbjct: 241 FIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAFLPSTFRDLFAFTILLMILWQRPTGLFGV 300 Query: 295 PEVEKV 300 + K+ Sbjct: 301 AKTTKI 306 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: 302 Number of extensions: 12 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: 306 Length adjustment: 27 Effective length of query: 273 Effective length of database: 279 Effective search space: 76167 Effective search space used: 76167 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