Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate 8502073 DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__Miya:8502073 Length = 596 Score = 141 bits (356), Expect = 4e-38 Identities = 79/206 (38%), Positives = 124/206 (60%), Gaps = 6/206 (2%) Query: 174 GGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASV 233 GGL +L+++ + I+VS +G+ + +GR S+ V ++ C ++IE+IRG PLI V+F Sbjct: 388 GGLAYSLLMAVIAISVSFFIGLAVGVGRSSSNRVFRIPCLLYIELIRGNPLIIVIFWVYF 447 Query: 234 MLPLFLPQGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKM 293 +P+ G T + F A ++ F AY+AE+VR G+Q IP GQ E A S GL++ Q M Sbjct: 448 FIPVMF--GTTLNVFWSATWALTAFTGAYIAEIVRTGIQNIPAGQVEAAYSTGLTYLQAM 505 Query: 294 GFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTG 353 IVLPQALK +IP IV FI +FKDTSL ++G+ +L + + N + P+ Sbjct: 506 RRIVLPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLELTFVAQ----GINNRLMIHPMEI 561 Query: 354 LIFAGFVFWLFCFGMSRYSGFMERLL 379 F++++ C+ MS ++ +ER L Sbjct: 562 YGTVAFLYFICCYSMSVFAARLERRL 587 Score = 103 bits (257), Expect = 1e-26 Identities = 60/164 (36%), Positives = 95/164 (57%), Gaps = 8/164 (4%) Query: 175 GLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVM 234 GL T+ +S + A++L LG +L L R S +++ T IE R PL+ LF Sbjct: 60 GLANTVRISLISSALALLLGTMLGLARLSLFRPLRVTATCVIEFFRNTPLLIQLFFWYFA 119 Query: 235 LPLFLPQG-------VTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGL 287 P LP + F+ F A IG+S++ +++MAEV+R GLQ+IPKG E A S GL Sbjct: 120 FPAILPDNAREALFSIQFE-FWCATIGLSIYTASFMAEVIRAGLQSIPKGLLEAAYSSGL 178 Query: 288 SFWQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDL 331 S++Q + I+LP A + +IP + + F+ K++SL ++G+ +L Sbjct: 179 SYFQVLRTIILPLAFRAIIPPLGSEFLNNMKNSSLAMVVGVAEL 222 Lambda K H 0.329 0.144 0.454 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: 586 Number of extensions: 31 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 384 Length of database: 596 Length adjustment: 34 Effective length of query: 350 Effective length of database: 562 Effective search space: 196700 Effective search space used: 196700 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 (21.8 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