Align Putrescine importer PuuP (characterized)
to candidate BWI76_RS10720 BWI76_RS10720 putrescine importer
Query= SwissProt::P76037 (461 letters) >FitnessBrowser__Koxy:BWI76_RS10720 Length = 463 Score = 838 bits (2164), Expect = 0.0 Identities = 421/454 (92%), Positives = 439/454 (96%), Gaps = 1/454 (0%) Query: 1 MAINSPLNIAAQPGKTRLRKSLKLWQVVMMGLAYLTPMTVFDTFGIVSGISDGHVPASYL 60 MAIN+ L+ A++ GK RLRKSLKLWQVVMMGLAYLTPMTVFDTFGIVSGIS+GHVPASYL Sbjct: 1 MAINTSLDNASEAGKPRLRKSLKLWQVVMMGLAYLTPMTVFDTFGIVSGISNGHVPASYL 60 Query: 61 LALAGVLFTAISYGKLVRQFPEAGSAYTYAQKSINPHVGFMVGWSSLLDYLFLPMINVLL 120 LALAGVLFTAISYGKLVRQFP+AGSAYTYAQKSI+PHVGFMVGWSSLLDYLFLPMINVLL Sbjct: 61 LALAGVLFTAISYGKLVRQFPQAGSAYTYAQKSISPHVGFMVGWSSLLDYLFLPMINVLL 120 Query: 121 AKIYLSALFPEVPPWVWVVTFVAILTAANLKSVNLVANFNTLFVLVQISIMVVFIFLVVQ 180 AKIYLSALFP+VPPWVWVVTFVAILTAANLKSVNLVANFNTLFVLVQISIMVVFI LVVQ Sbjct: 121 AKIYLSALFPDVPPWVWVVTFVAILTAANLKSVNLVANFNTLFVLVQISIMVVFIVLVVQ 180 Query: 181 GLHKGEGVGTVWSLQPFISENAHLIPIITGATIVCFSFLGFDAVTTLSEETPDAARVIPK 240 GLHKGEGVGTVWSLQPFIS+NAHLIPIITGATIVCFSFLGFDAVTTLSEETPDAARVIPK Sbjct: 181 GLHKGEGVGTVWSLQPFISQNAHLIPIITGATIVCFSFLGFDAVTTLSEETPDAARVIPK 240 Query: 241 AIFLTAVYGGVIFIAASFFMQLFFPDISRFKDPDAALPEIALYVGGKLFQSIFLCTTFVN 300 AIFLTAVYGGVIFIAASFFMQLFFPDISRFKDPDAALPEIALYVGGKLFQSIFLCTTFVN Sbjct: 241 AIFLTAVYGGVIFIAASFFMQLFFPDISRFKDPDAALPEIALYVGGKLFQSIFLCTTFVN 300 Query: 301 TLASGLASHASVSRLLYVMGRDNVFPERVFGYVHPKWRTPALNVIMVGIVALSALFFDLV 360 TLASGLASHASVSRLLYVMGRDNVFPER+FGYVHPKWRTPALNVIMVGIVALSALFFDLV Sbjct: 301 TLASGLASHASVSRLLYVMGRDNVFPERIFGYVHPKWRTPALNVIMVGIVALSALFFDLV 360 Query: 361 TATALINFGALVAFTFVNLSVFNHFWRRKGMNKSWKDHFHYLLMPLVGALTVGVLWVNLE 420 TATALINFGALVAFTFVNLSVFNHFWRRKG NK+WKD FHYLL+P+VGALTVGVLW+NLE Sbjct: 361 TATALINFGALVAFTFVNLSVFNHFWRRKGFNKTWKDRFHYLLLPMVGALTVGVLWINLE 420 Query: 421 STSLTLGLVWASLGGAYLWYLIRRYRK-VPLYDG 453 +TSLTLGL+WA LG YL YL RR+RK P +DG Sbjct: 421 ATSLTLGLIWAGLGLLYLTYLTRRFRKPPPQFDG 454 Lambda K H 0.328 0.141 0.437 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: 969 Number of extensions: 36 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: 461 Length of database: 463 Length adjustment: 33 Effective length of query: 428 Effective length of database: 430 Effective search space: 184040 Effective search space used: 184040 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 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