Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate WP_011842820.1 RSPH17029_RS20290 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >NCBI__GCF_000015985.1:WP_011842820.1 Length = 349 Score = 356 bits (913), Expect = e-103 Identities = 181/355 (50%), Positives = 247/355 (69%), Gaps = 11/355 (3%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60 MA + +++++K + G +I G+DLE+ D EFVV VGPSGCGKSTLLR++AGLEE++ G I Sbjct: 1 MAEISLRDVRKSYAGIEVIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAGEI 60 Query: 61 ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARI 120 + GR + + P +RD+AMVFQ YALYPHM+VR+NM++ L +A ++KAE+E++V+ +AR+ Sbjct: 61 AIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSARM 120 Query: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLH 180 LELG +L+RKP+QLSGGQRQRVA+GRA+VRNP FL DEPLSNLDA LRVQMRL++ L Sbjct: 121 LELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKELQ 180 Query: 181 KELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMG 240 + ++ T IYVTHDQVEAMT+AD++VV+N G EQ+ +P ++Y +PA FVAGF+G+P M Sbjct: 181 RTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPAMN 240 Query: 241 FLKGKITRVDSQGCEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHLELAKPGDCALQV 300 L R EV AG R+++P G + LG+RPEHL A P + ++ Sbjct: 241 MLP---ARGLGDALEV---AGQRLAVP-----APAGRDLILGVRPEHLHAAGPEEPGFEL 289 Query: 301 TADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFDAD 355 E LG+D F H R A G L +R G R + L + DA HLFDA+ Sbjct: 290 HVQAVEWLGADAFAHGRLADGTDLVLRTPGKAPVRERDRLKVAPDAAALHLFDAE 344 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: 399 Number of extensions: 11 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: 367 Length of database: 349 Length adjustment: 29 Effective length of query: 338 Effective length of database: 320 Effective search space: 108160 Effective search space used: 108160 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 Apr 10 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