Align Hexuronate transporter (characterized)
to candidate HSERO_RS20520 HSERO_RS20520 hexuronate transporter ExuT
Query= SwissProt::P0AA78 (432 letters) >FitnessBrowser__HerbieS:HSERO_RS20520 Length = 428 Score = 452 bits (1163), Expect = e-132 Identities = 218/422 (51%), Positives = 296/422 (70%), Gaps = 3/422 (0%) Query: 1 MRKIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTV 60 ++ IKGLRW++I LV LGT+ YL RN++ APTL +EL +STQQYSY++AA+ YT+ Sbjct: 1 LKTIKGLRWWIIVLVCLGTITNYLARNSLGVLAPTLKDELGMSTQQYSYVVAAFQVGYTI 60 Query: 61 MQPVAGYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGL 120 MQPV G+++D++G +IG+A+F VLW+V A A W LA R +G EAA IP+G+ Sbjct: 61 MQPVCGFIVDLIGLRIGFALFGVLWSVAGVLHAGATGWLSLAGFRALMGLTEAAAIPSGM 120 Query: 121 KASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMA 180 KA +EWFP KE+S+AVG+FN G+S+GAM+APPLV++ + + WQ AF+++G L F+WA Sbjct: 121 KAVAEWFPDKEKSVAVGWFNSGTSLGAMLAPPLVIFLQIRYGWQSAFVVTGILGFVWAAL 180 Query: 181 WLIFYKHPRDQKHLTDEERDYIINGQEAQHQVSTAK-KMSVGQILRNRQFWGIALPRFLA 239 W FY+ PRD L+D ER+ II+GQ VS + K V ++R+R+FW IAL RF A Sbjct: 181 WFAFYRSPRDHAALSDSERETIISGQ--LRPVSAVRGKRPVKDVVRSRRFWAIALARFFA 238 Query: 240 EPAWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLI 299 EPAW TF+ WIPL+ +LK IAMFAW+P L ADLG + GGYL P F + L+ Sbjct: 239 EPAWQTFSFWIPLYFVNERHLDLKSIAMFAWLPFLAADLGGLAGGYLSPFLINRFRIPLV 298 Query: 300 VSRKMVVTLGAVLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRNEV 359 SR V LGAV+MIGP +GL +PYVAI L C+GGFAHQ +SG + TLS+DVF EV Sbjct: 299 WSRVCGVVLGAVMMIGPACVGLVASPYVAIALFCVGGFAHQMISGLVNTLSADVFDPEEV 358 Query: 360 ATANGLTGMSAWLASTLFALVVGALADTIGFSPLFAVLAVFDLLGALVIWTVLQNKPAIE 419 TA+G GMSAW+ F+L+VGALADT+G+ PLF +L FDL+GA+++ +++ + E Sbjct: 359 GTASGFAGMSAWIGGLGFSLLVGALADTVGYGPLFGMLGAFDLIGAVLLIILIRGQSTEE 418 Query: 420 VA 421 A Sbjct: 419 RA 420 Lambda K H 0.326 0.138 0.437 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: 644 Number of extensions: 28 Number of successful extensions: 2 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: 432 Length of database: 428 Length adjustment: 32 Effective length of query: 400 Effective length of database: 396 Effective search space: 158400 Effective search space used: 158400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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