Align Putrescine importer PuuP (characterized)
to candidate PfGW456L13_4782 Amino acid transporters
Query= SwissProt::P76037 (461 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4782 Length = 441 Score = 375 bits (962), Expect = e-108 Identities = 194/433 (44%), Positives = 282/433 (65%), Gaps = 3/433 (0%) Query: 17 RLRKSLKLWQVVMMGLAYLTPMTVFDTFGIVSGISDGHVPASYLLALAGVLFTAISYGKL 76 RL+++L L VV+ G+AY+TP+ V TFGI++ + G VPA+YL AL + FTA+SYG++ Sbjct: 3 RLQRTLSLGSVVLFGIAYMTPIIVLGTFGILAQSTAGMVPAAYLAALVAMFFTAMSYGRM 62 Query: 77 VRQFPEAGSAYTYAQKSINPHVGFMVGWSSLLDYLFLPMINVLLAKIYLSALFPEVPPWV 136 FP AGSAY+Y +K+I+P +GF+ GW+ LLDYLFLPM L+ YL++ FP VP WV Sbjct: 63 ASAFPVAGSAYSYVRKAISPKLGFIAGWAVLLDYLFLPMAIWLIGAAYLNSAFPAVPQWV 122 Query: 137 WVVTFVAILTAANLKSVNLVANFNTLFVLVQISIMVVFIFLVVQGLHKGEGVGTVWSLQP 196 WV+ F++I +A N+ + L N L +LVQ +++ F+ L V + G+ +WS++P Sbjct: 123 WVLAFISITSAINIVGLKLANGINALLMLVQFLVLIAFVALCVHYV-GGDASTPLWSIKP 181 Query: 197 FISENAHLIPIITGATIVCFSFLGFDAVTTLSEETPDAARVIPKAIFLTAVYGGVIFIAA 256 F + + + I++GA I C+SFLGFDAV+TL+EET D R IP+AI L + GG+IF+ Sbjct: 182 FFNGDMQMPLIMSGAAIACYSFLGFDAVSTLTEETRDPRRTIPRAIMLITLIGGLIFVGV 241 Query: 257 SFFMQLFFPDISRFKDPDAALPEIALYVGGKLFQSIFLCTTFVNTLASGLASHASVSRLL 316 S+F+Q+ P +F D+A EIA +GG LF SIFL V ASGL++ AS SRLL Sbjct: 242 SYFVQIAHPSF-QFDSVDSAAYEIARNIGGDLFVSIFLIGLIVGQFASGLSAQASGSRLL 300 Query: 317 YVMGRDNVFPERVFGYVHPKWRTPALNVIMVGIVALSALFFDLVTATALINFGALVAFTF 376 Y MGRD V P+ FG +H ++ TP ++++ +VAL AL D+ T+T+ INFGA +AF+ Sbjct: 301 YAMGRDGVLPKSFFGTLHERFGTPINSILLCAVVALLALKLDVTTSTSFINFGAFLAFSL 360 Query: 377 VNLSVFNHFWRRKGMNKSWKDHFHYLLMPLVGALTVGVLWVNLESTSLTLGLVWASLGGA 436 VNLSV H+W G K ++ +LL P +G L V+L+ ++ LGL W ++G Sbjct: 361 VNLSVIFHYW-IGGEKKGPREFVLFLLFPFIGLSADLWLMVSLDHLAVYLGLSWLAIGVV 419 Query: 437 YLWYLIRRYRKVP 449 YL L +R+ P Sbjct: 420 YLAVLTGGFRRQP 432 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: 685 Number of extensions: 27 Number of successful extensions: 4 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: 441 Length adjustment: 33 Effective length of query: 428 Effective length of database: 408 Effective search space: 174624 Effective search space used: 174624 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