Align Amino-acid carrier protein, AlsT (characterized)
to candidate WP_008510473.1 BIBO1_RS17340 sodium:alanine symporter family protein
Query= TCDB::Q45068 (465 letters) >NCBI__GCF_000182725.1:WP_008510473.1 Length = 477 Score = 424 bits (1089), Expect = e-123 Identities = 225/472 (47%), Positives = 317/472 (67%), Gaps = 19/472 (4%) Query: 7 SLINIPSDFIWKY-LFYILIGLGLFFTIRFGFIQFRYFIEMFRIV---GEKPEGNKGVSS 62 ++I+ ++ W Y L Y L+ +G FFTIR F+QF +F E+FR+V G + E G+S Sbjct: 3 TIIDFLNNVFWNYILVYGLLAVGFFFTIRLKFVQFVHFPELFRVVFAAGRRDEA--GISP 60 Query: 63 MQAFFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKVRD 122 QA IS ASRVGTGN+TGVA+A+ GGPGA+FWMW+VA VG+A+++ ES LAQLYK+R+ Sbjct: 61 FQALTISIASRVGTGNITGVAVALYLGGPGAIFWMWIVALVGLATAYSESALAQLYKIRN 120 Query: 123 GE-DFRGGPAYYIQKGLGARWLGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNKIV 181 + +RGGPA+YI +GLG W G +F++ + +SFGL+FNAVQ N IA ++ AF++ K+ Sbjct: 121 QDGQYRGGPAFYIARGLGLPWAGALFSVCLILSFGLVFNAVQANAIADSMVMAFNMPKLG 180 Query: 182 VAIVLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIVKN 241 IVLA+L+ +IFGG++++ V++++VP MA YIL+A+ ++ N A P IA I + Sbjct: 181 TGIVLAILSGVVIFGGIRQIARVAEVVVPFMAFAYILMAICILAINFQAVPSTIALIFSS 240 Query: 242 ALGFEQVVGGGIGGI---IVIGAQRGLFSNEAGMGSAPNAAATAHVS--HPAKQGFIQTL 296 A G + VGG GGI ++ G +RGLFSNEAGMGSAPN AA A + HP+ QGF+Q+L Sbjct: 241 AFGLHEAVGGVTGGITAAMLNGVKRGLFSNEAGMGSAPNIAAVATPAPHHPSSQGFVQSL 300 Query: 297 GVFFDTFIICTSTAFIILLYSVTPKGDGI---QVTQAALNHHIGGWAPTFIAVAMFLFAF 353 GVF DT ++CT+TA +ILL + G G+ Q+TQ A+ HHIG FIA A+F FAF Sbjct: 301 GVFIDTILVCTATAIMILLSGILEPGSGLTGTQLTQMAMTHHIGDVGVYFIAAAIFFFAF 360 Query: 354 SSVVGNYYYGETNIEFIKT-SKTWLNIYRIAVIAMVVYGSLSGFQIVWDMADLFMGIMAL 412 +S++GNY Y E+ + F+ K + I R A++AMVV+G+ V+D AD MG+MA Sbjct: 361 TSIIGNYSYAESAMTFLGLGGKVPITILRCALLAMVVWGAYESIHTVFDAADASMGLMAT 420 Query: 413 INLIVIALLSNVAYKVYKDYAKQRKQGLDPVFKAKNIPGLK---NAETWEDE 461 INLI I LLS K+ DY QR+ G P F A + P L+ + E W ++ Sbjct: 421 INLIAIVLLSGTVKKLTVDYFAQRRAGQVPTFHAADYPELQGQIDMEIWSEQ 472 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: 591 Number of extensions: 28 Number of successful extensions: 7 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: 477 Length adjustment: 33 Effective length of query: 432 Effective length of database: 444 Effective search space: 191808 Effective search space used: 191808 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 24 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