Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate AO353_05475 AO353_05475 PTS fructose transporter subunit IIBC
Query= BRENDA::O31645 (650 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05475 Length = 579 Score = 382 bits (981), Expect = e-110 Identities = 206/472 (43%), Positives = 303/472 (64%), Gaps = 24/472 (5%) Query: 2 KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61 +L+A+T+CP G+AHT+MAAE LQ+AA RLG ++VETQG +G N L+ + I +AD +++ Sbjct: 121 RLVAVTACPTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLSAQAIADADVVLL 180 Query: 62 AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKAL-NGDIPVYRSATKSESGNHQEKKQ 120 AAD V +RF GKK+ G +++ E + KAL G S + + +K++ Sbjct: 181 AADIEVATERFAGKKIYRCGTGIALKQAEATLNKALAEGKQETASSGVQGPA----KKEK 236 Query: 121 NPIYRHLMNGVSFMVPFIVVGGLLIAVALTLG--GEKTPKGLVIPDDSFWKTIEQIGS-A 177 +Y+HL+ GVSFM+P +V GGL+IA++ G K P L + QIG Sbjct: 237 TGVYKHLLTGVSFMLPMVVAGGLMIALSFVFGITAFKEPGTLAA-------ALMQIGGDT 289 Query: 178 SFSFMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYA 237 +F M+P+LAGYIAYSIAD+PGL PGMIGG +A+T GAGF+GGIIAGF+AGYA Sbjct: 290 AFKLMVPLLAGYIAYSIADRPGLAPGMIGGLLAST-------LGAGFIGGIIAGFIAGYA 342 Query: 238 ALWIKKL-KVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGS 296 A I + ++P++++ + PI+IIP+ ASL GL ++++G PVA + SLT +L M + Sbjct: 343 AQAINRYARLPQSLEALKPILIIPLLASLFTGLVMIYVVGKPVAGLLESLTHFLDSMGTT 402 Query: 297 SSILLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIATF 356 ++ILL ++LG M+ D+GGP+NK A+ F ++ +Y M A +PPIGLGIATF Sbjct: 403 NAILLGVLLGGMMCVDLGGPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATF 462 Query: 357 LGKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNV 416 + +RKF ++RE GKAA +GL I+EGAIPFAA+DPLRVIP+ +AG ++M Sbjct: 463 IARRKFAQTEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIAGGALAGALSMYFGC 522 Query: 417 GDRVAHGGPIVAVL-GAVDHVLMFFIAVIAGSLVTALFVNVLKKDITASPVL 467 HGG V ++ A++H L++ +A++AGSL+TA+ +K+ A L Sbjct: 523 KLMAPHGGLFVMLIPNAINHALLYLLAIVAGSLLTAVVYAAVKRPEVAELAL 574 Score = 53.9 bits (128), Expect = 2e-11 Identities = 25/95 (26%), Positives = 51/95 (53%) Query: 1 MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAII 60 MKL +T+CPNG+ + + A L AA R G S VE E +L+ + +A+ ++ Sbjct: 1 MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEDAEWVL 60 Query: 61 IAADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQK 95 + + +V+ RF+GK++ ++ + ++++ Sbjct: 61 LVSTGTVDMSRFVGKRVFQSTPSQALQDVDAVLRR 95 Lambda K H 0.319 0.137 0.386 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: 770 Number of extensions: 45 Number of successful extensions: 6 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: 650 Length of database: 579 Length adjustment: 37 Effective length of query: 613 Effective length of database: 542 Effective search space: 332246 Effective search space used: 332246 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: 53 (25.0 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