Align Amino-acid carrier protein, AlsT (characterized)
to candidate SMc04263 SMc04263 amino acid carrier transmembrane protein
Query= TCDB::Q45068 (465 letters) >FitnessBrowser__Smeli:SMc04263 Length = 472 Score = 431 bits (1108), Expect = e-125 Identities = 227/470 (48%), Positives = 319/470 (67%), Gaps = 19/470 (4%) Query: 6 NSLINIPSDFIWKY-LFYILIGLGLFFTIRFGFIQFRYFIEMFRIVGEKPEGNK---GVS 61 +++I + W Y L Y L+ +GL+FT+R GF Q +F EMFR++ G+K G+S Sbjct: 2 DTIIGFLNTIFWGYVLIYGLLAVGLYFTVRLGFPQIVHFSEMFRVLSRG--GSKDAAGIS 59 Query: 62 SMQAFFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKVR 121 QA +S ASRVGTGNL GVA+A+ GGPGA FWMW+VA VGMA+++ ES LAQLYK+R Sbjct: 60 PFQALMVSLASRVGTGNLAGVAVALYLGGPGATFWMWIVAFVGMATAYAESALAQLYKIR 119 Query: 122 DGE-DFRGGPAYYIQKGLGARWLGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNKI 180 + + +RGGPA+YI +GL A W +F+ + +SFGL+FNAVQ N+IA A+ GAF V K+ Sbjct: 120 NEDGQYRGGPAFYIARGLNAPWAATIFSACLILSFGLVFNAVQANSIADAVQGAFGVPKL 179 Query: 181 VVAIVLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIVK 240 V + +A+L+ +IFGG++++ V++++VP MA Y+L A++V+I N +A PGV+ TI+ Sbjct: 180 AVGVAVALLSGVVIFGGIRQIARVAEIVVPFMAAAYLLTAVYVLIANASAVPGVLWTIIS 239 Query: 241 NALGFEQVVGGGIGGI---IVIGAQRGLFSNEAGMGSAPN--AAATAHVSHPAKQGFIQT 295 +A GF++ GG GGI ++ G +RGLFSNEAGMGSAPN A AT HP+ QGF+Q+ Sbjct: 240 SAFGFQEAAGGITGGIAAAMLNGVKRGLFSNEAGMGSAPNIAAVATPVPHHPSSQGFVQS 299 Query: 296 LGVFFDTFIICTSTAFIILLYSVTPKGDGI---QVTQAALNHHIGGWAPTFIAVAMFLFA 352 LGVF DT +ICT+T+ +ILL G G+ Q+TQAA++ HIG FIA+A+F FA Sbjct: 300 LGVFIDTILICTATSVMILLSGTLEPGSGVTGTQLTQAAMSTHIGSAGTYFIAIAIFFFA 359 Query: 353 FSSVVGNYYYGETNIEFI-KTSKTWLNIYRIAVIAMVVYGSLSGFQIVWDMADLFMGIMA 411 F+S++GNY Y E + ++ ++ L I R A +AMVV+G+ V+D AD MG+MA Sbjct: 360 FTSIIGNYSYAENALTYLGGGNRLGLMIMRCATLAMVVWGAYESITTVFDAADASMGLMA 419 Query: 412 LINLIVIALLSNVAYKVYKDYAKQRKQGLDPVFKAKNIPGLK---NAETW 458 INL+ I LLS K+ KDY +QRK G PVF A + P L+ + E W Sbjct: 420 TINLVAILLLSGTIAKLTKDYFEQRKAGAVPVFHAADYPELQGKIDGEIW 469 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: 576 Number of extensions: 24 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: 472 Length adjustment: 33 Effective length of query: 432 Effective length of database: 439 Effective search space: 189648 Effective search space used: 189648 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