Align ABC transporter for D-sorbitol, ATPase component (characterized)
to candidate Pf1N1B4_691 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::pseudo6_N2E2:Pf6N2E2_1960 (365 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_691 Length = 351 Score = 250 bits (639), Expect = 4e-71 Identities = 145/327 (44%), Positives = 197/327 (60%), Gaps = 14/327 (4%) Query: 1 MATLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTI 60 M L +EN++K + +K ++L + + + V F+GPSGCGK+TLLR+IAGLE +T G I Sbjct: 1 MTGLILENVEKHYGSACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLTGGEI 60 Query: 61 ELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARI 120 LDG DI +R+ MVFQ+ AL+PHMTV +N+++ L L G K D + +V E + Sbjct: 61 RLDGEDIGHTPAHQRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELLEL 120 Query: 121 LELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLH 180 ++L ++DR +LSGGQRQRVAI RAI PKI L DEPLS LDA LR ++E+ +L Sbjct: 121 IQLQEMIDRPVAKLSGGQRQRVAIARAIASRPKILLLDEPLSALDAKLRESMQVEIRQLQ 180 Query: 181 KELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMG 240 + L T I VTHDQ EAMT+A VVVL R++Q+GSP+E+Y HPAN FVA F+G+ + Sbjct: 181 QRLNITTIMVTHDQREAMTMADIVVVLGEHRVQQVGSPIEIYRHPANEFVADFIGSGNI- 239 Query: 241 FLQATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTLSAEGQVPVTT 300 A +V G L +P SS + VG+ V + IRPE L LS P T Sbjct: 240 -----FPATALGNGKVSLPGGDALQVPICSS-IVVGEKVKMLIRPEDLQLSQ----PQAT 289 Query: 301 DVTERLGSDTFCHVNVDSGESLTVRVQ 327 LG TF D G ++ V+ Sbjct: 290 AGNRLLGKVTFVR---DIGATIETTVE 313 Lambda K H 0.319 0.135 0.380 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: 291 Number of extensions: 8 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: 365 Length of database: 351 Length adjustment: 29 Effective length of query: 336 Effective length of database: 322 Effective search space: 108192 Effective search space used: 108192 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