Align Amino-acid carrier protein, AlsT (characterized)
to candidate GFF5497 PS417_28135 sodium:alanine symporter
Query= TCDB::Q45068 (465 letters) >FitnessBrowser__WCS417:GFF5497 Length = 481 Score = 399 bits (1026), Expect = e-116 Identities = 200/453 (44%), Positives = 292/453 (64%), Gaps = 8/453 (1%) Query: 8 LINIPSDFI-WKYLFYILIGLGLFFTIRFGFIQFRYFIEMFRIVGEKPEGNKG-VSSMQA 65 ++ + +DF+ K L +++GLG +FTIR F+Q R+F MF + + + + G +SS QA Sbjct: 1 MLEVINDFLSGKVLIVLIVGLGGYFTIRSRFVQLRHFFHMFSVFKDSLKSSAGQLSSFQA 60 Query: 66 FFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKVRDGED 125 +S A RVG GN+ GV +A+ GGPGAVFWMWV A VGM+SSF+E +L QLYK D E Sbjct: 61 LMLSLAGRVGAGNIAGVGIAVTLGGPGAVFWMWVTALVGMSSSFIECSLGQLYKRTDAEG 120 Query: 126 -FRGGPAYYIQKGLGARWLGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNKIVVAI 184 +RGGPAYYIQ GL RWLG+V A L+ V+FG FN +Q + + +L+ AF ++ + Sbjct: 121 TYRGGPAYYIQHGLQKRWLGMVMAFLLLVTFGFAFNGLQAHAVTHSLNNAFGLDTTYTGL 180 Query: 185 VLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIVKNALG 244 LAVL + GG+KR+ +++ L+VPV +YI + L+V++ P ++ATIVK+A G Sbjct: 181 ALAVLLGLVFIGGIKRIASIADLLVPVKTLVYIAVTLYVIVLQFDHVPAMLATIVKSAFG 240 Query: 245 FEQVVGGGIGGIIVIGAQRGLFSNEAGMGSAPNAAATAHVSHPAKQGFIQTLGVFFDTFI 304 +Q GG +G I++G +RG+F+NEAG+GSAPN AA A V HP QG +Q VF DTF+ Sbjct: 241 LDQAFGGLVGSAIIMGVKRGVFANEAGLGSAPNVAAVASVEHPIAQGVVQAFSVFLDTFV 300 Query: 305 ICTSTAFIILL---YSVTPKGDGIQVTQAALNHHIGGWAPTFIAVAMFLFAFSSVVGNYY 361 ICT TA +ILL Y+ +GDGI +TQ +L +G W FI+VA+ LF F+S++ NYY Sbjct: 301 ICTCTALLILLSGFYTPGFEGDGIALTQNSLAAVVGDWGRMFISVALALFVFTSIMYNYY 360 Query: 362 YGETNIEF-IKTSKTWLNIYRIAVIAMVVYGSLSGFQIVWDMADLFMGIMALINLIVIAL 420 GE+N+ F + ++ L YR V+ ++ +GS+ V+ AD+ M ++A +NL +A Sbjct: 361 LGESNLRFLVGNNRKVLMGYRALVLVLIFWGSIENLSTVFAFADITMTMLAFVNLFALAF 420 Query: 421 LSNVAYKVYKDYAKQRKQGL-DPVFKAKNIPGL 452 L +A ++ DY QR G+ PVF + P L Sbjct: 421 LFKIAMRILNDYDNQRAAGIKTPVFDSSQFPDL 453 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: 556 Number of extensions: 33 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: 465 Length of database: 481 Length adjustment: 33 Effective length of query: 432 Effective length of database: 448 Effective search space: 193536 Effective search space used: 193536 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