Align Low-affinity putrescine importer PlaP (characterized)
to candidate BWI76_RS18905 BWI76_RS18905 putrescine/spermidine ABC transporter
Query= SwissProt::P0AA47 (452 letters) >FitnessBrowser__Koxy:BWI76_RS18905 Length = 452 Score = 804 bits (2076), Expect = 0.0 Identities = 398/452 (88%), Positives = 425/452 (94%) Query: 1 MSHNVTPNTSRVELRKTLTLVPVVMMGLAYMQPMTLFDTFGIVSGLTDGHVPTAYAFALI 60 MSHN TP TSRVELRKTLTL+PVVMMGLAYMQPMTLFDTFGIVSGLTDGHV TAYAFALI Sbjct: 1 MSHNATPKTSRVELRKTLTLIPVVMMGLAYMQPMTLFDTFGIVSGLTDGHVATAYAFALI 60 Query: 61 AILFTALSYGKLVRRYPSAGSAYTYAQKSISPTVGFMVGWSSLLDYLFAPMINILLAKIY 120 AILFTALSYGKLVRR+PSAGSAYTYAQKSISP VGFMVGWSSLLDYLF PMINILLAKIY Sbjct: 61 AILFTALSYGKLVRRFPSAGSAYTYAQKSISPAVGFMVGWSSLLDYLFMPMINILLAKIY 120 Query: 121 FEALVPSIPSWMFVVALVAFMTAFNLRSLKSVANFNTVIVVLQVVLIAVILGMVVYGVFE 180 FEALVPSIPSW+FVVALVAFMT NLRS+K+VANFNT+IV+LQ+ ++AVI+G+++YGV Sbjct: 121 FEALVPSIPSWIFVVALVAFMTISNLRSIKTVANFNTLIVILQMGIVAVIVGLIIYGVMH 180 Query: 181 GEGAGTLASTRPFWSGDAHVIPMITGATILCFSFTGFDGISNLSEETKDAERVIPRAIFL 240 GEGAGTL STRPFWS AHV+PMITGATILCFSF GFDGIS+LSEETKDAERVIP+AIFL Sbjct: 181 GEGAGTLTSTRPFWSEGAHVVPMITGATILCFSFLGFDGISSLSEETKDAERVIPKAIFL 240 Query: 241 TALIGGMIFIFATYFLQLYFPDISRFKDPDASQPEIMLYVAGKAFQVGALIFSTITVLAS 300 TALIGG+IFI A+YFLQLYFPDISRFKDPDASQPEIMLYVAGK FQ G LIFS++TVLAS Sbjct: 241 TALIGGLIFIGASYFLQLYFPDISRFKDPDASQPEIMLYVAGKTFQWGVLIFSSVTVLAS 300 Query: 301 GMAAHAGVARLMYVMGRDGVFPKSFFGYVHPKWRTPAMNIILVGAIALLAINFDLVMATA 360 GMAAHAGV+RLMYVMGRDGVFP FFGYVHPKWRTPA N++LVGAIALLAI FDLV ATA Sbjct: 301 GMAAHAGVSRLMYVMGRDGVFPTRFFGYVHPKWRTPAWNVLLVGAIALLAIKFDLVTATA 360 Query: 361 LINFGALVAFTFVNLSVISQFWIREKRNKTLKDHFQYLFLPMCGALTVGALWVNLEESSM 420 LINFGALVAFTFVNLSVISQFWIREKRNKTLKDHF YL LP+CGALTVGALW+NLEESSM Sbjct: 361 LINFGALVAFTFVNLSVISQFWIREKRNKTLKDHFNYLILPVCGALTVGALWINLEESSM 420 Query: 421 VLGLIWAAIGLIYLACVTKSFRNPVPQYEDVA 452 VLGLIW IGL+YLACVTKSFRNPVPQYEDVA Sbjct: 421 VLGLIWGGIGLVYLACVTKSFRNPVPQYEDVA 452 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: 797 Number of extensions: 21 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: 452 Length adjustment: 33 Effective length of query: 419 Effective length of database: 419 Effective search space: 175561 Effective search space used: 175561 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