Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate AO353_05485 AO353_05485 PTS fructose transporter subunit IIA
Query= reanno::pseudo3_N2E3:AO353_05485 (953 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05485 Length = 953 Score = 1827 bits (4732), Expect = 0.0 Identities = 953/953 (100%), Positives = 953/953 (100%) Query: 1 MLELTIEQISMGQSAVDKAAALHLLADTLVNDGLVAEGYLSGLQAREAQGSTFLGQGIAI 60 MLELTIEQISMGQSAVDKAAALHLLADTLVNDGLVAEGYLSGLQAREAQGSTFLGQGIAI Sbjct: 1 MLELTIEQISMGQSAVDKAAALHLLADTLVNDGLVAEGYLSGLQAREAQGSTFLGQGIAI 60 Query: 61 PHGTPDTRDLVHTTGVRLLQFPEGVDWGDGHIVYLAIGIAAKSDEHLRLLQLLTRALGET 120 PHGTPDTRDLVHTTGVRLLQFPEGVDWGDGHIVYLAIGIAAKSDEHLRLLQLLTRALGET Sbjct: 61 PHGTPDTRDLVHTTGVRLLQFPEGVDWGDGHIVYLAIGIAAKSDEHLRLLQLLTRALGET 120 Query: 121 DLGQALRRASSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180 DLGQALRRASSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS Sbjct: 121 DLGQALRRASSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180 Query: 181 NGFSAVLQQVEALPLGDGLWWLHSEQTVKRPGLAFVTPDKPIRYLGQPLSGLFCLASLGE 240 NGFSAVLQQVEALPLGDGLWWLHSEQTVKRPGLAFVTPDKPIRYLGQPLSGLFCLASLGE Sbjct: 181 NGFSAVLQQVEALPLGDGLWWLHSEQTVKRPGLAFVTPDKPIRYLGQPLSGLFCLASLGE 240 Query: 241 AHQALLERLCALLIEGRGHELGRATSRRAVLEVLGGELPADWPSARIALANAHGLHARPA 300 AHQALLERLCALLIEGRGHELGRATSRRAVLEVLGGELPADWPSARIALANAHGLHARPA Sbjct: 241 AHQALLERLCALLIEGRGHELGRATSRRAVLEVLGGELPADWPSARIALANAHGLHARPA 300 Query: 301 KILAQLAKSFEGEIRIRIVDGQDSAVSVKSLSKLLSLGARRGQVLELIAEPSIAADALPA 360 KILAQLAKSFEGEIRIRIVDGQDSAVSVKSLSKLLSLGARRGQVLELIAEPSIAADALPA Sbjct: 301 KILAQLAKSFEGEIRIRIVDGQDSAVSVKSLSKLLSLGARRGQVLELIAEPSIAADALPA 360 Query: 361 LLRAIEEGLGEDIEPLPTVSAQSEVIDEITDVVVAPASGCVIQAVAAAPGIAIGPAHIQV 420 LLRAIEEGLGEDIEPLPTVSAQSEVIDEITDVVVAPASGCVIQAVAAAPGIAIGPAHIQV Sbjct: 361 LLRAIEEGLGEDIEPLPTVSAQSEVIDEITDVVVAPASGCVIQAVAAAPGIAIGPAHIQV 420 Query: 421 LQAIDYPLRGESTAIERERLKTSLADVRRDIEGLIQRSKAKAIREIFITHQEMLDDPELT 480 LQAIDYPLRGESTAIERERLKTSLADVRRDIEGLIQRSKAKAIREIFITHQEMLDDPELT Sbjct: 421 LQAIDYPLRGESTAIERERLKTSLADVRRDIEGLIQRSKAKAIREIFITHQEMLDDPELT 480 Query: 481 DEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLAERAADLRDIGRRVLAQLCGIETP 540 DEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLAERAADLRDIGRRVLAQLCGIETP Sbjct: 481 DEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLAERAADLRDIGRRVLAQLCGIETP 540 Query: 541 SEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAV 600 SEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAV Sbjct: 541 SEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAV 600 Query: 601 LRLASGTPLLLDGQRGRLHVDADAATLQRAAEERDNREQRLQAAAAQRHQPALTTDGHAV 660 LRLASGTPLLLDGQRGRLHVDADAATLQRAAEERDNREQRLQAAAAQRHQPALTTDGHAV Sbjct: 601 LRLASGTPLLLDGQRGRLHVDADAATLQRAAEERDNREQRLQAAAAQRHQPALTTDGHAV 660 Query: 661 EVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAHQQAPDEATQEVEYRRVLDGLAGRPL 720 EVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAHQQAPDEATQEVEYRRVLDGLAGRPL Sbjct: 661 EVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAHQQAPDEATQEVEYRRVLDGLAGRPL 720 Query: 721 VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIM 780 VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIM Sbjct: 721 VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIM 780 Query: 781 FPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND 840 FPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND Sbjct: 781 FPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND 840 Query: 841 LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL 900 LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL Sbjct: 841 LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL 900 Query: 901 VGLGVDELSVSARSIGEVKARVRELSLAQVKHLAQLALAVGSANEVRALVEAL 953 VGLGVDELSVSARSIGEVKARVRELSLAQVKHLAQLALAVGSANEVRALVEAL Sbjct: 901 VGLGVDELSVSARSIGEVKARVRELSLAQVKHLAQLALAVGSANEVRALVEAL 953 Lambda K H 0.319 0.135 0.383 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: 2482 Number of extensions: 68 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: 953 Length of database: 953 Length adjustment: 44 Effective length of query: 909 Effective length of database: 909 Effective search space: 826281 Effective search space used: 826281 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 (21.7 bits) S2: 57 (26.6 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