Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate HSERO_RS22730 HSERO_RS22730 sugar ABC transporter substrate-binding protein
Query= uniprot:A0A165KPY4 (416 letters) >FitnessBrowser__HerbieS:HSERO_RS22730 Length = 446 Score = 223 bits (568), Expect = 9e-63 Identities = 134/400 (33%), Positives = 200/400 (50%), Gaps = 11/400 (2%) Query: 19 SASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGGGDSAMTVLKSRVISG 78 + + G ++VLH+WTS E +++ + + + WRD A+ GG G A VLKS V++ Sbjct: 48 ATATGSLQVLHWWTSASERQAINVVVNQLAKQDIQWRDVAIPGGAGMGAAKVLKSMVLAN 107 Query: 79 NPPSAAQTKGPAIQEWASEGVLANMDTLAKAEKWDELLPKVVADVMKYKGAYVAAPVNVH 138 P Q G EWA G+L +D +A W++ + V ++ G VAAP+ +H Sbjct: 108 RAPEVTQLNGVVFGEWADLGLLLELDNVAVQGNWEKQMFPTVWSLLNNHGHVVAAPLGIH 167 Query: 139 RVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHGGQNWQDFTTFESVVL 198 R+N ++ + K+ ++ PKTWDEF KL+ +G+VP+A + WQ T FE++ L Sbjct: 168 RINSLYYNVAVFKRYNLSP-PKTWDEFDQIVKKLQGSGVVPLAQSAEAWQLATLFENLAL 226 Query: 199 GVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPGRDWNLATAMLIQGKA 258 G +Y+ V++ A M L+ R + G R W ++ G+A Sbjct: 227 AESGPAYYRKLFVEMSPAAYLDARMLHILKRLRALAGAMAQPVRERPWTEVARSMVSGEA 286 Query: 259 GFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFILFKLKDAAAQKAQSDL 318 +MGDWAKGE A G + F CA APG+ ++ D+ +F + A Q Q L Sbjct: 287 AMLIMGDWAKGELNAWGMEVDQQFGCAPAPGTGEYHLYSTDTLAMF-AGNYAHQPMQETL 345 Query: 319 ASSIMSPAFQEVFNLNKGSIPV-RAGQPMDKFDDCAKASAKDFVDTAKSGGL--VPSAAH 375 A MSPA Q +N KGSIPV RA P D CA+ S + F G + PS H Sbjct: 346 ARLTMSPAVQSEYNRIKGSIPVLRAADP--HMDRCARDSWRTF----SKGPMWQAPSLVH 399 Query: 376 GMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAKT 415 MA T+ AI V +F+ D +S A K++A A+T Sbjct: 400 RMATDDTTKDAIVAEVQRFFMDRSISEEQAQKRLATIART 439 Lambda K H 0.315 0.128 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: 501 Number of extensions: 28 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: 416 Length of database: 446 Length adjustment: 32 Effective length of query: 384 Effective length of database: 414 Effective search space: 158976 Effective search space used: 158976 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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