Align Amino-acid carrier protein, AlsT (characterized)
to candidate PP_0496 PP_0496 Sodium/alanine symporter
Query= TCDB::Q45068 (465 letters) >FitnessBrowser__Putida:PP_0496 Length = 480 Score = 395 bits (1015), Expect = e-114 Identities = 207/452 (45%), Positives = 291/452 (64%), Gaps = 7/452 (1%) Query: 8 LINIPSDFI-WKYLFYILIGLGLFFTIRFGFIQFRYFIEMFRIVGEKPEGNKG-VSSMQA 65 ++ + +DF+ K L +++GLG +FTIR F+QFR+F MF + E G G +SS QA Sbjct: 1 MLEVINDFLSGKLLIVLIVGLGSYFTIRSRFVQFRHFTHMFSVFKESLRGQAGQLSSFQA 60 Query: 66 FFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKVRDGED 125 +S A RVG GN+ GV +A+ GGPGAVFWMWV A VGM+SSF E TLAQ+YK DG+ Sbjct: 61 LMLSLAGRVGAGNIAGVGIAVTLGGPGAVFWMWVTALVGMSSSFFECTLAQVYKRADGDG 120 Query: 126 -FRGGPAYYIQKGLGARWLGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNKIVVAI 184 +RGGPAYYIQ GL + + IVF+IL+ V++G F +Q+ T+ +L AF + I Sbjct: 121 LYRGGPAYYIQHGLKRKSMAIVFSILLLVTYGFAFIGLQSYTVTHSLQNAFAFDPSHTGI 180 Query: 185 VLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIVKNALG 244 VLAVL A GG+KR+ AVS L+VPV YI + L+V+ T I P ++ TI K+A G Sbjct: 181 VLAVLLAITFIGGIKRIAAVSDLLVPVKTLAYIGVTLYVIGTQIEHVPAMLETIFKSAFG 240 Query: 245 FEQVVGGGIGGIIVIGAQRGLFSNEAGMGSAPNAAATAHVSHPAKQGFIQTLGVFFDTFI 304 + G +G IV+G +RG+F+NEAG+GSAPN AA A V HP QG +Q VF DTF+ Sbjct: 241 LDPAFAGLLGSAIVMGVKRGVFANEAGLGSAPNVAAVAAVKHPGAQGVVQAFSVFLDTFV 300 Query: 305 ICTSTAFIILL---YSVTPKGDGIQVTQAALNHHIGGWAPTFIAVAMFLFAFSSVVGNYY 361 ICT TA +ILL Y+ +GDGI +TQ +L +G W F++VA+ LF F+ ++ NYY Sbjct: 301 ICTCTALLILLSGFYTPGFEGDGIVLTQNSLAAVVGDWGRVFVSVALSLFVFTCILYNYY 360 Query: 362 YGETNIEFIKTSKTWLNIYRIAVIAMVVYGSLSGFQIVWDMADLFMGIMALINLIVIALL 421 GE +++F+ ++ L ++R V+A+VV+GS+ V+ AD+ M +A +NL+ +ALL Sbjct: 361 LGENSLQFLSRNRVVLMVFRGLVLALVVWGSMQDLSTVFAFADITMTCLAFVNLVALALL 420 Query: 422 SNVAYKVYKDYAKQRKQGL-DPVFKAKNIPGL 452 V +V +DY QRK G+ PVF + L Sbjct: 421 FKVGLRVMRDYDDQRKAGVKQPVFDSSKFADL 452 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: 560 Number of extensions: 25 Number of successful extensions: 4 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