Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate 8500415 DvMF_1165 inner-membrane translocator (RefSeq)
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Miya:8500415 Length = 306 Score = 218 bits (555), Expect = 1e-61 Identities = 125/309 (40%), Positives = 193/309 (62%), Gaps = 11/309 (3%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVAL-ITFLAIGS 59 ME F+Q L N L G+ Y LIA+GYT+VYG++ +INFAHG+I+M+GA++A ++ L +G Sbjct: 1 MEIFIQNLFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYIAFFVSSLLLGD 60 Query: 60 L-GIT----WVPLALLVMLVASMLFTAVYGWTVERIAYRPLR--SSPRLAPLISAIGMSI 112 L G+ W LAL V L +ML TA G T+ERIAYRPLR + RL +I+A+ + Sbjct: 61 LLGVFNLPGWAALALTVPL--TMLLTAGVGVTLERIAYRPLRRKGAHRLYVVITALMCGL 118 Query: 113 FLQNYVQILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTS 172 L+N L GA + L P + + G+VSV+ +++ I+ + + ++TRT Sbjct: 119 ILENGNLALLGASRRKL-PDMVDKVVYTFGSVSVTNLKVWVIITAFLVFFLLQFIVTRTR 177 Query: 173 LGRAQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAG 232 +G A RA DK L+G+ +D +I TFV+G+ A +AG++ + Y ++D Y+G + G Sbjct: 178 IGMAMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVG 237 Query: 233 VKAFTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGL 292 KAF AAV+GGIG + GA +GG ++ IE + ++ S ++D+ FTIL+++L RPTGL Sbjct: 238 WKAFIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAFLPSTFRDLFAFTILLMILWQRPTGL 297 Query: 293 LGRPEIEKV 301 G + K+ Sbjct: 298 FGVAKTTKI 306 Lambda K H 0.329 0.144 0.425 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: 300 Number of extensions: 17 Number of successful extensions: 3 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: 301 Length of database: 306 Length adjustment: 27 Effective length of query: 274 Effective length of database: 279 Effective search space: 76446 Effective search space used: 76446 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