Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate WP_008347408.1 BA79_RS16380 amino acid permease
Query= TCDB::P40812 (497 letters) >NCBI__GCF_000691145.1:WP_008347408.1 Length = 448 Score = 330 bits (846), Expect = 6e-95 Identities = 170/438 (38%), Positives = 258/438 (58%), Gaps = 13/438 (2%) Query: 30 MGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVLHRP 89 + NR VQ+IAIGG IGTGLFLG+G +Q+AGP++ YLI G+ FF++RALGEL+L + Sbjct: 10 LSNRHVQLIAIGGTIGTGLFLGSGKAIQLAGPSIIFAYLIVGMAIFFVMRALGELLLSKA 69 Query: 90 SSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWVFAL 149 S A ++LG A++V GW Y+ W MT + D+ AV +Y+ YW D+PQW+ A+ Sbjct: 70 GYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWF---DIPQWIPAI 126 Query: 150 GALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLEGNATGFHLIT 209 L I+ N++ VK F EMEFWFALIKV+ I++ + VG + L G + + Sbjct: 127 ICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAGPVTVTNLW 186 Query: 210 DNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIGLFYV 269 +GG FP+G+ L+ Q V+FA+ +ELVG +A E +PQK +P AIN + RI FYV Sbjct: 187 SHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIPLRILFFYV 246 Query: 270 GSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGLYCTGRI 329 G++ +L+ + PW A +SPFV F +G+P ++N VVLT+A S+ NSG++ T RI Sbjct: 247 GAIFVLLCINPWTELSASESPFVKTFGLIGIPVAAGLINFVVLTSAASACNSGMFSTSRI 306 Query: 330 LRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLNFASLGI 389 L ++S P ++++ VP + + +V VG L+ L+P + F IV +++ Sbjct: 307 LYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLIPEQAFGIVTTISAICF 366 Query: 390 IASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAFDYPNGTY 449 I W+ I++C ++ ++ E A +FK P PF + L+ ++LV+M F Sbjct: 367 IWVWSIILICHLKYKKTRPELHKAS-TFKAPFTPFVNIAVLVLFAAILVIMLF------- 418 Query: 450 TIASLPLIAILLVAGWFG 467 A A+LL WFG Sbjct: 419 --ADATRPALLLTPVWFG 434 Lambda K H 0.328 0.140 0.434 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: 602 Number of extensions: 35 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: 497 Length of database: 448 Length adjustment: 33 Effective length of query: 464 Effective length of database: 415 Effective search space: 192560 Effective search space used: 192560 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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