Align Amino-acid carrier protein, AlsT (characterized)
to candidate 202642 SO3541 sodium:alanine symporter family protein (NCBI ptt file)
Query= TCDB::Q45068 (465 letters) >FitnessBrowser__MR1:202642 Length = 488 Score = 431 bits (1109), Expect = e-125 Identities = 218/457 (47%), Positives = 310/457 (67%), Gaps = 11/457 (2%) Query: 7 SLINIPSDFIW-KYLFYILIGLGLFFTIRFGFIQFRYFIEMFRIVGEKPEG-NKGVSSMQ 64 +++N + +W K L Y L+G GL+FT+R FIQ +F +I+ +G G+SS Q Sbjct: 4 TIVNFLNALLWGKLLVYGLVGAGLYFTLRLVFIQLTHFKHSLKIMTMSRQGCESGLSSFQ 63 Query: 65 AFFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKVRDGE 124 F S A+RVG GN+ GVA+AI GPGAVFWMW++A +GMA++ VESTLAQ+YKVRD Sbjct: 64 VFCTSMAARVGAGNMAGVAVAIGAAGPGAVFWMWLIAMLGMATAMVESTLAQVYKVRDAN 123 Query: 125 -DFRGGPAYYIQKGLGARWLGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNKIVVA 183 FRGGP+YY++KGLG RW+G++FA + ++FGL+FNAVQ NTI GA++ F + V Sbjct: 124 GQFRGGPSYYMEKGLGQRWMGVLFAFFLIIAFGLVFNAVQANTITGAMERVFGFDPTYVG 183 Query: 184 IVLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIVKNAL 243 I L + + F+I GGL++V VS+ IVP+MA YILIA +V+ N+ P VI+ IVK+A Sbjct: 184 IGLVLASGFVIMGGLRKVARVSEFIVPIMALAYILIAFIIVLFNLEQLPAVISLIVKSAF 243 Query: 244 GFEQVVGGGIGGIIV----IGAQRGLFSNEAGMGSAPNAAATA--HVSHPAKQGFIQTLG 297 G+++ GG+ + G RGLFSNEAGMGSA N AA+A + +HPA QGF+Q +G Sbjct: 244 GWQEAAAGGVAYTVAQAMQAGIARGLFSNEAGMGSAANVAASASPNPNHPASQGFVQMMG 303 Query: 298 VFFDTFIICTSTAFIILLY-SVTPKGDGIQVTQAALNHHIGGWAPTFIAVAMFLFAFSSV 356 VF DT +ICT+TA IILL + DGI++T A+++H+G W FIAVA+FLF F+S+ Sbjct: 304 VFVDTIVICTATAAIILLSGDIGSSDDGIRLTINAMSNHVGDWGGAFIAVAIFLFCFTSI 363 Query: 357 VGNYYYGETNIEFIKTSKT-WLNIYRIAVIAMVVYGSLSGFQIVWDMADLFMGIMALINL 415 + NY Y ETN+ F+ + T L ++R+ V+ MV++GS++ +VW++AD+ MG+MA +N+ Sbjct: 364 IANYSYAETNVMFLTGNSTKALPLFRLCVLGMVMFGSVAKISLVWNLADVSMGLMATVNI 423 Query: 416 IVIALLSNVAYKVYKDYAKQRKQGLDPVFKAKNIPGL 452 + + LLS +A +V DY Q K G P F P L Sbjct: 424 VALLLLSGLAIRVINDYCDQLKSGKMPEFDRSKFPEL 460 Lambda K H 0.327 0.142 0.426 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: 595 Number of extensions: 26 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: 465 Length of database: 488 Length adjustment: 33 Effective length of query: 432 Effective length of database: 455 Effective search space: 196560 Effective search space used: 196560 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