Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate Pf1N1B4_4847 Various polyols ABC transporter, ATP-binding component
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4847 Length = 367 Score = 298 bits (764), Expect = 1e-85 Identities = 166/359 (46%), Positives = 231/359 (64%), Gaps = 11/359 (3%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M+ L+I+N++K + +KGID+ + EF+V +G SGCGKSTLL +IAGL E SGG I Sbjct: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 + R + V P RD+AMVFQ+YALYP++SV +N+ F L++ V +AE +K V + AR+ Sbjct: 61 ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVGEAARI 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 L++ +L+RKP QLSGGQRQRVAIGRA+VRNP++FLFDEPLSNLDA LR++MR EL RLH Sbjct: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLH 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 + L+ T++YVTHDQ+EAMT+A ++ V+ G+IEQ+ +P ++Y +PA L+VAGF+G+P M Sbjct: 181 KELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMG 240 Query: 241 ILDAEMT-ANGLKIE-----GCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQ 294 L ++T NG E G LPL A G V +GIRPE L LA + Sbjct: 241 FLKGKVTRVNGQSCEVLLDAGTRITLPLSGA---NLSVGGAVTLGIRPEHLELAQPGDC- 296 Query: 295 RLTASVEVVELTGPE-LVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPE 352 L + +V E G + T + +T + A G + D HLFD + Sbjct: 297 TLQVTADVSERLGSDTFCHVLTSSGEALTMRVRGDLASRYGETLSLHLDAEHCHLFDAD 355 Lambda K H 0.320 0.136 0.385 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: 358 Number of extensions: 14 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: 360 Length of database: 367 Length adjustment: 29 Effective length of query: 331 Effective length of database: 338 Effective search space: 111878 Effective search space used: 111878 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