Align Amino-acid carrier protein, AlsT (characterized)
to candidate 14152 b0007 predicted transporter (NCBI)
Query= TCDB::Q45068 (465 letters) >FitnessBrowser__Keio:14152 Length = 476 Score = 372 bits (954), Expect = e-107 Identities = 206/480 (42%), Positives = 289/480 (60%), Gaps = 27/480 (5%) Query: 3 SFFNSLINIPSDFIW-KYLFYILIGLGLFFTIRFGFIQFRYFIEMFRIVGEKPEGNKG-V 60 SF NS++ W + Y+L G G +FT R GF+QFRY + + + G + Sbjct: 6 SFINSVL-------WGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNSIHPQPGGL 58 Query: 61 SSMQAFFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKV 120 +S Q+ S A+RVG+GNL GVALAI GGPGAVFWMWV A +GMA+SF E +LAQLYK Sbjct: 59 TSFQSLCTSLAARVGSGNLAGVALAITAGGPGAVFWMWVAAFIGMATSFAECSLAQLYKE 118 Query: 121 RD-GEDFRGGPAYYIQKGLGARWLGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNK 179 RD FRGGPA+Y+ +GLG RW+G++FA+ + +++G+IF+ VQ N +A AL +F Sbjct: 119 RDVNGQFRGGPAWYMARGLGMRWMGVLFAVFLLIAYGIIFSGVQANAVARALSFSFDFPP 178 Query: 180 IVVAIVLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIV 239 +V I+LAV T I GL V + Q VP+MA I++L +L + + NI P VI +I Sbjct: 179 LVTGIILAVFTLLAITRGLHGVARLMQGFVPLMAIIWVLTSLVICVMNIGQLPHVIWSIF 238 Query: 240 KNALGFEQVVGGGIG----GIIVIGAQRGLFSNEAGMGSAPNAAATA--HVSHPAKQGFI 293 ++A G+++ GG G I G QR +FSNEAGMGS PNAAA A HPA QG + Sbjct: 239 ESAFGWQEAAGGAAGYTLSQAITNGFQRSMFSNEAGMGSTPNAAAAAASWPPHPAAQGIV 298 Query: 294 QTLGVFFDTFIICTSTAFIILLY---SVTPKGDGIQVTQAALNHHIGGWAPTFIAVAMFL 350 Q +G+F DT +ICT++A +ILL + +GIQ+ Q A+ +G W F+ + + L Sbjct: 299 QMIGIFIDTLVICTASAMLILLAGNGTTYMPLEGIQLIQKAMRVLMGSWGAEFVTLVVIL 358 Query: 351 FAFSSVVGNYYYGETNIEFIKTSK---TWLNIYRIAVIAMVVYGSLSGFQIVWDMADLFM 407 FAFSS+V NY Y E N+ F++ + W RI A V+ G+L ++W +AD+ M Sbjct: 359 FAFSSIVANYIYAENNLFFLRLNNPKAIW--CLRICTFATVIGGTLLSLPLMWQLADIIM 416 Query: 408 GIMALINLIVIALLSNVAYKVYKDYAKQRKQGLDPVFKAKNIPGL---KNAETWEDEKQE 464 MA+ NL I LLS V + + DY +QRK G+ PVF P + + + W+D QE Sbjct: 417 ACMAITNLTAILLLSPVVHTIASDYLRQRKLGVRPVFDPLRYPDIGRQLSPDAWDDVSQE 476 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: 539 Number of extensions: 24 Number of successful extensions: 8 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: 476 Length adjustment: 33 Effective length of query: 432 Effective length of database: 443 Effective search space: 191376 Effective search space used: 191376 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