Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= TCDB::Q97Q42 (385 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 363 bits (933), Expect = e-105 Identities = 192/364 (52%), Positives = 252/364 (69%), Gaps = 4/364 (1%) Query: 3 KPIIEFKNVSKVFEDSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTG 62 K IIE +VSK F D L D+ +++G+F T+LG SG GK+T+L +IAG A+ G Sbjct: 7 KSIIEVSHVSKFFGDKTA--LDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEG 64 Query: 63 DIMLDGVRINDIPTNKRDVHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQRVAEVL 122 +I + G I P +KR V+TVFQ YALFPH+NV++N+AF L+L+K K+ I ++V L Sbjct: 65 EIRISGKEITQTPPHKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAAL 124 Query: 123 KMVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYELRE 182 KMV + YE R + LSGGQ+QRVAIARAI+N+P V+LLDEPL+ALDLK+R DMQ EL+E Sbjct: 125 KMVGMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKE 184 Query: 183 LQQRLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATFIGESN 242 + + LGITFV+VTHDQEEAL +SD I VM++G+I Q GTP+DIY+EPIN FVA FIGESN Sbjct: 185 MHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGESN 244 Query: 243 ILPGTMIEDYLVEFNGKRFEAVDGGMKPNEPVEVVIRPEDLRI-TLPEEGKLQVKVDTQL 301 IL GTMI D LV F G FE VD G N PV+VVIRPEDL I + E +L V T + Sbjct: 245 ILNGTMIHDKLVRFCGTEFECVDEGFGENTPVDVVIRPEDLYIFPVSEMAQLTGVVQTSI 304 Query: 302 FRGVHYEIIAYDELGNEWMIHSTRKAIVGEEIGLDFEPEDIHIMRLNETEEEFDARIEEY 361 F+GVHYE+ G E+++ VG E+GL +P DIHIM+ F+ ++++ Sbjct: 305 FKGVHYEMTVLCG-GYEFLVQDYHHFEVGAEVGLLVKPFDIHIMKKERVCNTFEGKLQDA 363 Query: 362 VEIE 365 +E Sbjct: 364 THVE 367 Score = 39.7 bits (91), Expect = 2e-07 Identities = 35/176 (19%), Positives = 75/176 (42%), Gaps = 4/176 (2%) Query: 178 YELRELQQRLGI--TFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVA 235 + + E+ Q G+ T +F E + + F++ D + G V + +P + + Sbjct: 288 FPVSEMAQLTGVVQTSIFKGVHYEMTVLCGGYEFLVQDYHHFEVGAEVGLLVKPFDIHIM 347 Query: 236 TFIGESNILPGTMIEDYLVEFNGKRFEAVD-GGMKPNEPVEVVIRPEDLRITLPEE-GKL 293 N G + + VEF G FE G++ V+V + + + + EE G L Sbjct: 348 KKERVCNTFEGKLQDATHVEFLGCTFECASVEGLESGTDVKVEVDFDKVILQDNEEDGTL 407 Query: 294 QVKVDTQLFRGVHYEIIAYDELGNEWMIHSTRKAIVGEEIGLDFEPEDIHIMRLNE 349 +V L++G HY + + + + + G+ +G+ P+ I ++++ + Sbjct: 408 TGEVKFILYKGDHYHLTVWSDWDENVFVDTNDVWDDGDRVGITIPPDAIRVIKITD 463 Lambda K H 0.318 0.138 0.386 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: 543 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 385 Length of database: 463 Length adjustment: 32 Effective length of query: 353 Effective length of database: 431 Effective search space: 152143 Effective search space used: 152143 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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