Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate SMc00273 SMc00273 transmembrane protein
Query= reanno::SB2B:6938090 (466 letters) >FitnessBrowser__Smeli:SMc00273 Length = 419 Score = 246 bits (627), Expect = 1e-69 Identities = 145/451 (32%), Positives = 245/451 (54%), Gaps = 45/451 (9%) Query: 10 LFLCML-LGMPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAIPFFILSSA 68 LF +L + +P+ AL ++ IL +KL++ T + + LLAIPFFILS + Sbjct: 8 LFAALLAISVPVGYALIIAAGAAILWQGGTPTVLAVVKLFQPT-QSFPLLAIPFFILSGS 66 Query: 69 FLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIVGMV 128 + +G + ++++ FA VG GG+ +V+ +F VSGS+ A +A+GS++I Sbjct: 67 LMMSGTLGQKLVQFAAALVGRFHGGMGQVTVVGSTIFGGVSGSAVAEASALGSMLIPWQK 126 Query: 129 RAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLLMGVLLMV 188 + GYP FAA V +S T+ LIPPSI +++++ S A +F A ++PGL++ +M+ Sbjct: 127 KEGYPAGFAAAVTASSSTIAGLIPPSIPLILFSTVANSSIASLFSAAVLPGLMLAGGMMI 186 Query: 189 AIYIVARIKNLPSRPFPG-VKALSLSSAKAMGGLALIFIVLGSIYGGVASPTEAAAVACV 247 Y+ RI+N P G +K+ S A+ LA+ F ++ + G+A+PTE + +A Sbjct: 187 VCYLSGRIRNFPRLTDAGQLKSFGRSMLSALPALAMPFFIILLLRAGIATPTEVSVIAVF 246 Query: 248 YAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLIKTPTDKEIRNVVRDGA 307 YA LV++ YRD+ W E I AA+V ++ G Sbjct: 247 YALLVSLLLYRDL------TW----ERIYAALVGTVITTG-------------------- 276 Query: 308 KVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWG----FLIIVNLLLLAAGN 363 +++ +IA + L HVL TER+P I+A W L G ++++NL++L G Sbjct: 277 ----VVMLVIAASSLVGHVLITERVPTIVA----NWALETLGSAILIILMMNLIMLVVGM 328 Query: 364 FMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITGRS 423 F++ A +L++ P I +G+DPI LG+++ +N+ IG+ TPP+G LF+ A I Sbjct: 329 FLDLPAAILLLGPTFVAIGHAIGMDPIQLGVMICINLSIGLFTPPIGTTLFIGAVIARVP 388 Query: 424 IGWVIHACLPWLLLLLGFLVLITYVPQISLF 454 IG V+ P+ ++ LVL++YVP ++++ Sbjct: 389 IGAVVKELWPFYIVAAAVLVLMSYVPALTIY 419 Lambda K H 0.329 0.144 0.424 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: 571 Number of extensions: 45 Number of successful extensions: 5 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: 466 Length of database: 419 Length adjustment: 32 Effective length of query: 434 Effective length of database: 387 Effective search space: 167958 Effective search space used: 167958 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 (21.8 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