Align Negative regulator of SacY activity; PTS system sac EIIBC component; EC 2.7.1.- (characterized)
to candidate BWI76_RS19555 BWI76_RS19555 PTS beta-glucoside transporter subunit EIIBCA
Query= SwissProt::P15400 (459 letters) >FitnessBrowser__Koxy:BWI76_RS19555 Length = 619 Score = 214 bits (544), Expect = 8e-60 Identities = 139/433 (32%), Positives = 214/433 (49%), Gaps = 22/433 (5%) Query: 2 HKEIAKELLLLAGGKNNIISISHCTTRLRFDVKDETKIDIHAIENLQGVQGTFFRYGLFQ 61 +K +A+++L GG+ NI+S+ HC TRLRF +KD K D ++ GV G FQ Sbjct: 3 YKALAQDILTRVGGRENIVSLVHCATRLRFKLKDSKKADAEGLKANPGVIMVVESGGQFQ 62 Query: 62 IIFGAGVVNKIYKEVVHVWETAPSE-------EPVHQKKASRKLNPAAAFAKTLSDIFVP 114 ++ G V VW SE EPV K K++ +S IF P Sbjct: 63 VVIG--------NHVHDVWLAVRSEAGLTDDSEPVAVK--GEKVSLIGQLIDIVSGIFTP 112 Query: 115 IIPAITASGLLMGLIGMIKVFHWFAAGSPWIKMLDLVSSTAFILLPILVGFSAARQFGSN 174 I + ASG+L GL+ + V W K+ S F P+ +G++A ++FG N Sbjct: 113 FIGVLAASGILKGLLALAVVCGWLTTQQATYKIWFAASDALFFFFPLFLGYTAGKKFGGN 172 Query: 175 PYLGAVIAGLLTHPDLLDPSMLGSKTPSSLDIWGLHIPM--MGYQGSMIPILLSVFVMSK 232 P++ VI G LTHP L+ + S P + + L IP+ + Y S+IPI+L+ +V Sbjct: 173 PFITMVIGGALTHP-LMIQAFDASMAPGAATEYFLGIPVTFINYSSSVIPIILASWVSCW 231 Query: 233 IEKLLKSIVPKSLDVVIIPFITVMVTGCLALIVMNPAASIIGQIMTQSIVYIYDHAGIAA 292 IEK +I+P S+ P I + V L +++ P A+ + Q++ IY A A Sbjct: 232 IEKRSNAILPSSMKNFFTPAICLAVVVPLTFLIIGPVATWLSQLLANGYQLIYQVAPWLA 291 Query: 293 GALFGGIYSTIVLSGLHHSFYAIEATLLANPHVGVNFLVPIWSMANVAQGGAGLAVFLKT 352 GA G ++ V+ GLH + LA +G + ++P+ A + Q GA L +FL+T Sbjct: 292 GAAMGALWQVCVIFGLHWGLIPLMINNLA--VLGHDSMMPMLLPAVMGQVGAALGIFLRT 349 Query: 353 KQSSLKKIALPASLTAFLGIVEPIVFGVNLKLIRPFIGAAIGGAIGGAYVVAVQVVANSY 412 + + K +A A G+ EP ++G+NL L RPFI + GAIGGA V S+ Sbjct: 350 RDARQKVLAGSAVSAGIFGVTEPAIYGLNLPLRRPFIFGCVAGAIGGAMVGFSDSHVYSF 409 Query: 413 GLTGIPMISIVLP 425 G I ++ ++P Sbjct: 410 GFGNIFTLAQMIP 422 Lambda K H 0.325 0.141 0.415 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: 739 Number of extensions: 40 Number of successful extensions: 4 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: 459 Length of database: 619 Length adjustment: 35 Effective length of query: 424 Effective length of database: 584 Effective search space: 247616 Effective search space used: 247616 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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