Align Low-affinity putrescine importer PlaP (characterized)
to candidate 203165 SO4081 amino acid permease (NCBI ptt file)
Query= SwissProt::P0AA47 (452 letters) >FitnessBrowser__MR1:203165 Length = 443 Score = 568 bits (1465), Expect = e-167 Identities = 277/432 (64%), Positives = 337/432 (78%) Query: 14 LRKTLTLVPVVMMGLAYMQPMTLFDTFGIVSGLTDGHVPTAYAFALIAILFTALSYGKLV 73 L+++L L VV+MGLAY+ PM +FDTFGIVS +T GHV T+Y AL ILFTA SYG LV Sbjct: 8 LKQSLNLWQVVVMGLAYLTPMAVFDTFGIVSEITSGHVATSYLLALAGILFTAFSYGHLV 67 Query: 74 RRYPSAGSAYTYAQKSISPTVGFMVGWSSLLDYLFAPMINILLAKIYFEALVPSIPSWMF 133 R+YP AGSAYTYAQK+ SP VGFMVGWSSLLDY+F PMIN+LLAKIY A+ P++ W+F Sbjct: 68 RKYPYAGSAYTYAQKNFSPNVGFMVGWSSLLDYMFMPMINMLLAKIYLTAMFPNVEPWIF 127 Query: 134 VVALVAFMTAFNLRSLKSVANFNTVIVVLQVVLIAVILGMVVYGVFEGEGAGTLASTRPF 193 + LV MT NLR + VANFN VIV Q+ +I V +G++ + + GEG G +AS RPF Sbjct: 128 IFGLVTVMTVLNLRGIDLVANFNGVIVFAQIAIILVFIGLMAHSLSLGEGEGVIASVRPF 187 Query: 194 WSGDAHVIPMITGATILCFSFTGFDGISNLSEETKDAERVIPRAIFLTALIGGMIFIFAT 253 +S + P+ TGATILCFSF GFDG+S+LSEETKDA+RVIPRAI LTALIGG+IF+ + Sbjct: 188 YSEQVTLAPLFTGATILCFSFLGFDGLSSLSEETKDAKRVIPRAILLTALIGGVIFVSVS 247 Query: 254 YFLQLYFPDISRFKDPDASQPEIMLYVAGKAFQVGALIFSTITVLASGMAAHAGVARLMY 313 YFLQLYFPDISRF+ DA PEI LYV G FQ L+ +TI VLASGMAAHAGVAR++Y Sbjct: 248 YFLQLYFPDISRFEQLDAVLPEIALYVGGNLFQSIVLVATTIAVLASGMAAHAGVARILY 307 Query: 314 VMGRDGVFPKSFFGYVHPKWRTPAMNIILVGAIALLAINFDLVMATALINFGALVAFTFV 373 VMGRD + P FGYVHPKWRTPA N++LVG +AL A++FDL MA AL+NFGALVAFTFV Sbjct: 308 VMGRDNMLPNKGFGYVHPKWRTPAFNVVLVGLLALSAVSFDLEMALALVNFGALVAFTFV 367 Query: 374 NLSVISQFWIREKRNKTLKDHFQYLFLPMCGALTVGALWVNLEESSMVLGLIWAAIGLIY 433 NLSVI QF+I+EKRN++LK+H QY LP+CGA T+G LW+NLE S+ LGLIW A+G++Y Sbjct: 368 NLSVIVQFYIKEKRNQSLKEHLQYFVLPLCGAATIGVLWINLEPQSLELGLIWGAVGMLY 427 Query: 434 LACVTKSFRNPV 445 LA + R V Sbjct: 428 LALRSLRLRKAV 439 Lambda K H 0.328 0.140 0.424 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: 627 Number of extensions: 15 Number of successful extensions: 1 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: 452 Length of database: 443 Length adjustment: 33 Effective length of query: 419 Effective length of database: 410 Effective search space: 171790 Effective search space used: 171790 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: 51 (24.3 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