Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate PfGW456L13_1799 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1799 Length = 351 Score = 248 bits (633), Expect = 2e-70 Identities = 144/314 (45%), Positives = 200/314 (63%), Gaps = 15/314 (4%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60 M+ L ++N++K + +K ++L + + + V F+GPSGCGK+TLLR+IAGLE +SGG I Sbjct: 1 MSGLILENVEKHYGSACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGGEI 60 Query: 61 ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARI 120 LDG DI R+ MVFQ+ AL+PHM+V +N+++ L L GV+KA+ + +V E + Sbjct: 61 RLDGEDIGHTPAHLRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELLEL 120 Query: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLH 180 ++L M+ R +LSGGQRQRVAI RAI +PKI L DEPLS LDA LR M++E+ +L Sbjct: 121 IQLQAMINRPVAKLSGGQRQRVAIARAIANHPKILLLDEPLSALDAKLRESMQVEIRQLQ 180 Query: 181 KELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMG 240 + L T I VTHDQ EAMTMAD VVVL K++QVG+P+++Y PAN FVA F+G+ Sbjct: 181 QRLNITTIMVTHDQREAMTMADIVVVLGEHKVQQVGTPIEIYRHPANEFVADFIGS---- 236 Query: 241 FLKGKITRVDSQG-CEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHLELAKPGDCALQ 299 G I G +V L G + +P+ + VG V + IRPE L+L+ P Q Sbjct: 237 ---GNIFPATVLGNGKVSLPGGDALQVPICS-SIVVGEKVKMLIRPEDLQLSAP-----Q 287 Query: 300 VTADVSERLGSDTF 313 TA + LG TF Sbjct: 288 ATAG-NRLLGKVTF 300 Lambda K H 0.320 0.137 0.389 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: 328 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: 367 Length of database: 351 Length adjustment: 29 Effective length of query: 338 Effective length of database: 322 Effective search space: 108836 Effective search space used: 108836 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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