Align Amino-acid carrier protein, AlsT (characterized)
to candidate 6936729 Sama_0916 sodium:alanine symporter family protein (RefSeq)
Query= TCDB::Q45068 (465 letters) >FitnessBrowser__SB2B:6936729 Length = 480 Score = 437 bits (1123), Expect = e-127 Identities = 219/457 (47%), Positives = 315/457 (68%), Gaps = 11/457 (2%) Query: 7 SLINIPSDFIW-KYLFYILIGLGLFFTIRFGFIQFRYFIEMFRIVG-EKPEGNKGVSSMQ 64 +++N + +W K L Y L+G GL+FT+R FIQ +F +++ + G+ G+SS Q Sbjct: 4 TIVNFLNALLWGKLLVYGLVGAGLYFTVRLAFIQLTHFKHGIKVMTISRQGGDGGLSSFQ 63 Query: 65 AFFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKVRDGE 124 F S A+RVG GN+ GVA+AI T GPGAVFWMW +A +GMA++ +ESTLAQ+YKV+D + Sbjct: 64 VFCTSMAARVGAGNMAGVAVAIGTAGPGAVFWMWAIAVLGMATAMIESTLAQVYKVKDED 123 Query: 125 -DFRGGPAYYIQKGLGARWLGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNKIVVA 183 FRGGPAYY++KGLG RW+G +F++ + ++FGL+FNAVQ NTI GAL+ F I V Sbjct: 124 GQFRGGPAYYMEKGLGQRWMGALFSVFLILAFGLVFNAVQANTITGALERVFGFEPIYVG 183 Query: 184 IVLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIVKNAL 243 I + V + F+I GGL++V VS+++VP MA +Y+LIA VV+ N+ P V + I+K+A Sbjct: 184 IGIVVASGFVIMGGLRKVARVSEIVVPFMALVYLLIASVVVVVNLDKLPEVFSLIIKSAF 243 Query: 244 GFEQVVGGGIGGIIV----IGAQRGLFSNEAGMGSAPN--AAATAHVSHPAKQGFIQTLG 297 G+++ V GG+ + G RGLFSNEAGMGSA N A+AT + +HPA QGF+Q +G Sbjct: 244 GWQEAVAGGVAYSVAQAMQAGIARGLFSNEAGMGSAANVAASATPNPNHPASQGFVQMMG 303 Query: 298 VFFDTFIICTSTAFIILLY-SVTPKGDGIQVTQAALNHHIGGWAPTFIAVAMFLFAFSSV 356 VF DT +ICT+TA IILL + + DGI++T AL H+G W FIA A+FLF F+S+ Sbjct: 304 VFVDTLVICTATAAIILLAGDMGAESDGIKLTIDALTSHVGDWGGAFIAFAIFLFCFTSI 363 Query: 357 VGNYYYGETNIEFIK-TSKTWLNIYRIAVIAMVVYGSLSGFQIVWDMADLFMGIMALINL 415 + NY Y ETN+ F+ KT L ++R+ V+ MV++G+++ +VWD+AD+ MG+MA++N+ Sbjct: 364 IANYSYAETNVMFLSGNRKTALPLFRLLVLGMVMFGAMAKISLVWDLADVSMGLMAIVNI 423 Query: 416 IVIALLSNVAYKVYKDYAKQRKQGLDPVFKAKNIPGL 452 I + LLS +A +V DY +Q K+G PVF P L Sbjct: 424 IALVLLSGLAIRVIDDYREQLKKGDMPVFDRSKFPEL 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: 614 Number of extensions: 28 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: 480 Length adjustment: 33 Effective length of query: 432 Effective length of database: 447 Effective search space: 193104 Effective search space used: 193104 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