Align Amino-acid carrier protein, AlsT (characterized)
to candidate 354002 BT4476 amino acid carrier protein (NCBI ptt file)
Query= TCDB::Q45068 (465 letters) >FitnessBrowser__Btheta:354002 Length = 462 Score = 468 bits (1204), Expect = e-136 Identities = 243/461 (52%), Positives = 322/461 (69%), Gaps = 9/461 (1%) Query: 7 SLINIPSDFIWKYLFYI-LIGLGLFFTIRFGFIQFRYFIEMFRIVGEKP----EGNKGVS 61 + IN +D +W Y+ I L+G ++F+IR F+QFR EM ++ E +G K VS Sbjct: 2 NFINEINDILWTYILIIMLLGCAVWFSIRTRFVQFRMLREMIILLSESAGKGKQGEKHVS 61 Query: 62 SMQAFFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKVR 121 S QAF I+ ASRVGTGNL GVA AIA GGPGAVFWMWV+A +G +S+F+ESTLAQLYK+R Sbjct: 62 SFQAFAITIASRVGTGNLAGVATAIAIGGPGAVFWMWVIALLGASSAFIESTLAQLYKIR 121 Query: 122 DGEDFRGGPAYYIQKGLGARWLGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNKIV 181 + F GGPAYY++KGL W+GI+FA+LI+++FG FN+VQ+NTI A + AF N V Sbjct: 122 GKDSFVGGPAYYMKKGLKQPWMGILFAVLISITFGFAFNSVQSNTICAAAEHAFGFNHTV 181 Query: 182 VAIVLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIVKN 241 + VL LT IIFGG++R+ VS +IVPVMA Y+ +AL +V+ NIT P VI+ I+ + Sbjct: 182 LGGVLTALTLVIIFGGIRRIAHVSSIIVPVMALGYVGLALVIVLLNITHLPEVISLIISH 241 Query: 242 ALGFEQVVGGGIGGIIVIGAQRGLFSNEAGMGSAPNAAATAHVSHPAKQGFIQTLGVFFD 301 A G+EQ +GGG+G ++ G +RGLFSNEAGMGSAPNAAATA+V+HP KQG IQTL VF D Sbjct: 242 AFGWEQALGGGVGMALMQGIKRGLFSNEAGMGSAPNAAATANVTHPVKQGLIQTLAVFTD 301 Query: 302 TFIICTSTAFIILLYSVTPKG--DGIQVTQAALNHHIGGWAPTFIAVAMFLFAFSSVVGN 359 T + CT TAFIIL G +G+Q+TQ AL + IG F+AVA+F FAFSS++GN Sbjct: 302 TLLNCTCTAFIILFSGAPLDGSSNGVQLTQQALTNEIGASGSIFVAVALFFFAFSSILGN 361 Query: 360 YYYGETNIEFIKTSKTWLNIYRIAVIAMVVYGSLSGFQIVWDMADLFMGIMALINLIVIA 419 YYYGE NI FI K L+ YRI V MV++GS++ +VW +AD+ M +MA+ NLI I Sbjct: 362 YYYGEANIRFITAKKWVLHTYRILVSGMVLFGSVATLDLVWSLADITMALMAVCNLIAII 421 Query: 420 LLSNVAYKVYKDYAKQRKQGL-DPVFKAKNIPGL-KNAETW 458 L A ++ DY Q+K G+ PVF+ + +P + K+ E W Sbjct: 422 FLGKYAIRLLSDYRAQKKAGIQSPVFRKETMPDIEKDLECW 462 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: 600 Number of extensions: 25 Number of successful extensions: 2 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: 462 Length adjustment: 33 Effective length of query: 432 Effective length of database: 429 Effective search space: 185328 Effective search space used: 185328 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