Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Pf1N1B4_1243 ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1243 Length = 521 Score = 261 bits (666), Expect = 6e-74 Identities = 176/501 (35%), Positives = 260/501 (51%), Gaps = 20/501 (3%) Query: 1 MSDMSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILS 60 MS+ + P L LR I K +PG A ++L+ GE+HAL+GENGAGKSTLMKI+ Sbjct: 1 MSNPVPIPDQIPRLQLRRISKRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIY 60 Query: 61 GAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRG 120 G AD GE GQRV + P AR LG+ +++Q SL LSVA+NI L Sbjct: 61 GVTHAD-SGEMIWQGQRVTMRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGT 119 Query: 121 LVARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTP 180 +R + R G P V SLSI +RQ VEI R + + R+L++DEPT+ Sbjct: 120 PKQLEPKIREVSQ---RYGMALEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSV 176 Query: 181 LSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQA 240 L+ E D LF +R+L EG +IL+ISH++ E+ L TVLR G G A S Sbjct: 177 LTPQEADELFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDR 236 Query: 241 ALVKMMVGR--DLSGFYTKTHGQAVEREVMLSVRDVA------DGRRVKGCSFDLRAGEV 292 L ++MVG +L Y K G + LSV ++ G +K FD+R+GE+ Sbjct: 237 QLAQLMVGEAAELITDYPKVMG----ADAFLSVTGLSWHNPDPFGCSLKNIDFDVRSGEI 292 Query: 293 LGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLT 352 +G+AG+ G G+ EL L+ G + R + + G P + G+A++ Sbjct: 293 VGVAGVAGNGQDELLALLSGEERLPRDDSATISFGGQPVAHLRPDARRK----LGLAFVP 348 Query: 353 EDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNV 412 +R G + S+ +N L + + G + R + + I G++ + Sbjct: 349 AERLGHGAVPELSLADNALLTAFQQGLVSHGLVQRGKVQALAEDIIRRFGVKTPDSLAPA 408 Query: 413 GALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISS 472 +LSGGN QK +L R + QP++L+ PT GVD+GA + I+R + AL +G AIL+IS Sbjct: 409 RSLSGGNLQKFILGREILQQPKLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISE 468 Query: 473 ELPEVVGLCDRVLVMREGTLA 493 +L E+ +CDR+ + G L+ Sbjct: 469 DLDELFQICDRLGALCGGQLS 489 Score = 74.3 bits (181), Expect = 1e-17 Identities = 73/247 (29%), Positives = 109/247 (44%), Gaps = 26/247 (10%) Query: 278 RRVKGC------SFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGG 331 +R GC + GE+ L G GAG++ L ++++G GE+ G Sbjct: 21 KRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEM-----IWQGQ 75 Query: 332 LVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAAR 391 VT+ P QA GI + + L F SV +NI L A+G Sbjct: 76 RVTMR--NPAQARGLGIGMVFQHFSL---FETLSVAQNIAL------AMGAAAGTPKQLE 124 Query: 392 RRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKS 451 + E G+ + ++ V +LS G +Q+V + R L R+LILDEPT + Sbjct: 125 PKIREVSQRYGMALEPERL-VHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEAD 183 Query: 452 EIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIA 511 E++ + LA G +IL IS +L EV LC V+R G +AG PA + ++ Sbjct: 184 ELFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAQC---SDRQLAQ 240 Query: 512 LATGAAA 518 L G AA Sbjct: 241 LMVGEAA 247 Lambda K H 0.320 0.136 0.382 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: 663 Number of extensions: 32 Number of successful extensions: 8 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: 540 Length of database: 521 Length adjustment: 35 Effective length of query: 505 Effective length of database: 486 Effective search space: 245430 Effective search space used: 245430 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: 52 (24.6 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