Align protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized)
to candidate BWI76_RS07290 BWI76_RS07290 PTS beta-glucoside transporter subunit EIIBCA
Query= BRENDA::P12655 (664 letters) >FitnessBrowser__Koxy:BWI76_RS07290 Length = 626 Score = 303 bits (776), Expect = 2e-86 Identities = 209/667 (31%), Positives = 338/667 (50%), Gaps = 57/667 (8%) Query: 1 MDYSKVASEVITAVG-KDNLVAAAHCATRLRLVLKDDSKVDQKALDKNADVKGTFKTDGQ 59 M+Y++ A +++ AVG +N+ HCATRLR+ D +KV+ + V + GQ Sbjct: 1 MNYNETADKILHAVGGAENIRMLTHCATRLRMEFNDRAKVNDAQIGTLPGVISVVEKGGQ 60 Query: 60 YQVIIGPGDVNFVYDEIIKQTGLTEVSTDDLKKIAASGKKFNP---IMALIKLLSDIFVP 116 +Q++IG +V VY + K + + K A K P + +I ++S F P Sbjct: 61 FQIVIG-NEVQQVYRRLNK-------ALPEKKGPAGGDKNAKPAGIVARIISVISTTFTP 112 Query: 117 IIPALVAGGLLMALNNFLTSEGLFGTKSLVQQFPIIKGSSDMIQLMSAAPFWFLPILVGI 176 +IPA+ G++ AL L G+ S Q ++ +++ A F+FLP+L+ Sbjct: 113 VIPAITGAGMIKALLAILKLTGVISETSSTYQ---------LLNIIADAAFFFLPVLLAY 163 Query: 177 SAAKRFGANQFLGASIGMIMVAPGAANIIGLAANAPISKAATIGAYTGFWNIFGLHVTQA 236 A+ +F N L ++ +++ PG + LAA + + G++V + Sbjct: 164 GASLKFECNPILAMTLAGVLLHPGIGQM--LAAGKAV-------------DFVGINVLLS 208 Query: 237 SYTYQVIPVLVAVWLLSILEKFFHKRLPSAVDFTFTPLLSVIITGFLTFIVIGPVMKEVS 296 Y V+P+++ VWL+S +E+F K PS + F P+L ++IT L +V+GP ++ Sbjct: 209 DYAGSVLPIILTVWLMSWVERFAEKVSPSIIKFFVKPMLILLITAPLALVVVGPAGILLN 268 Query: 297 DWLTNGIVWLYDTTGFLGMGVFGALYSPVVMTGLHQSFPAIETQLISAFQNGTGHGDFIF 356 D + G + +L + G L +++TG + I T +S +G + Sbjct: 269 DLVAAGAGAIDRHASWLIPMLMGTLQPFLIITGTAWAMTPIATGQLSKSGYEMINGPGML 328 Query: 357 VTASMANVAQGAATFAIYFLTKDKKMKGLSSSSGVSALLGITEPALFGVNLKYRFPFFCA 416 + NVA GAAT + TK+ ++ L+SSSG +ALLGITEPAL+GV LK+R A Sbjct: 329 AS----NVAMGAATLCVALKTKNSNLRQLASSSGFTALLGITEPALYGVLLKFRRVLIAA 384 Query: 417 LIGSASA---AAIAGLLQVVAVSLGSAGFLGFLSIKASSIPFYVVCELISFAIAFAVTYG 473 +IG A A ++GL++ VS G A F+ +I +V IS + F +T+ Sbjct: 385 MIGGGCAGVYAGVSGLVRYAFVSPGLAALPAFIGENPMNIVHALVTCAISIVVTFTLTW- 443 Query: 474 YGKTKAVDVFAAEAAVEEAIEEVQEIPEEAASAANKAQVTDEVLAAPLAGEAVELTSVND 533 F A V E EEV E P+ A S N+ + + +PL G+ V L+ VND Sbjct: 444 ---------FIAFKDVPEEQEEVGEAPQPAVSPKNEGETE---VFSPLRGQVVALSEVND 491 Query: 534 PVFSSEAMGKGIAIKPSGNTVYAPVDGTVQIAFDTGHAYGIKSDNGAEILIHIGIDTVSM 593 VFS +G+G+AI+P + AP GTV + + HA G++SD+G E+LIHIGIDTV++ Sbjct: 492 DVFSGGLLGEGLAIRPEEGVLRAPFSGTVMMFLPSCHAVGLQSDSGLELLIHIGIDTVNL 551 Query: 594 EGKGFEQKVQADQKIKKGDVLGTFDSDKIAEAGLDNTTMFIVTNTADYASVETLASSGTV 653 G+ F ++ +++ G L FD I +AG D T IV N + S+ L ++ V Sbjct: 552 NGQHFSSTLKVGDRVEAGQELIRFDIPAIEQAGYDLITPVIVVNGDEQHSLR-LTAAAQV 610 Query: 654 AVGDSLL 660 G+ L+ Sbjct: 611 DYGEQLM 617 Lambda K H 0.320 0.135 0.384 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: 797 Number of extensions: 33 Number of successful extensions: 6 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: 664 Length of database: 626 Length adjustment: 38 Effective length of query: 626 Effective length of database: 588 Effective search space: 368088 Effective search space used: 368088 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: 54 (25.4 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