Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate YP_004143814.1 Mesci_4655 polar amino acid ABC transporter inner membrane subunit
Query= uniprot:Q31RN9 (396 letters) >NCBI__GCF_000185905.1:YP_004143814.1 Length = 385 Score = 216 bits (551), Expect = 7e-61 Identities = 140/410 (34%), Positives = 213/410 (51%), Gaps = 91/410 (22%) Query: 16 AWLRQNLFSSWLNSAITLLLVVIIVTVVGRLGLWITTEARWT--------------VLVD 61 AW+R+NL +S ++ +T++ + ++ ++ ++ W A WT + D Sbjct: 28 AWVRKNLIASTGDTILTIVGIALVAMILPQIINWAFINAVWTGPDRTVCATVAQGGIQPD 87 Query: 62 NWT------------LFFVGRYPAAEQWR----LWLWLGLLSPTLGLTWGCLATGSHRWQ 105 WT F +GRYP E+WR L++ LL P L Sbjct: 88 GWTGACWAFVNAKFGQFMLGRYPIEERWRPILVAILFVALLVPML--------------- 132 Query: 106 RRSLWGWAGLAAAIAGIPLPWFPHKLGLAAIAATVPAASWLAQRCRGQAWLRFLPTLWGV 165 +P P K GL A+ L+ V Sbjct: 133 ------------------MPKVPRK-GLNAVL------------------------LFFV 149 Query: 166 LFLVGLWLLQGGL-GLRPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIR 224 L +V LL GG+ GL V ++ W GLL+TL+ + + + SLPLGI+LALGR+S +P I+ Sbjct: 150 LPIVAFVLLVGGMFGLPHVETSLWGGLLVTLSLSFVGIAVSLPLGIVLALGRRSKMPIIK 209 Query: 225 WLSVTYIELFRGLPLVTILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRG 284 L V +IE RG+PL+T+LFF VM+PL L D+ LRA++G+++F +AY+AE VRG Sbjct: 210 TLCVVFIETVRGIPLITVLFFASVMLPLFLPEGVSFDKFLRALIGVSLFAAAYMAEVVRG 269 Query: 285 GLQAIPQGQFEAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLL 344 GLQAIP+GQ+E A +LGL +Q FIV+PQAL++ IP IV F+ + +DT+L+ I+ + Sbjct: 270 GLQAIPKGQYEGADSLGLGYWQKMYFIVMPQALKLVIPGIVNTFIGMFKDTSLVIIISMF 329 Query: 345 ELLGISRSIL--ANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392 +LLGI + AN A +F ++WL C+G+++ S E+RL Sbjct: 330 DLLGIVKQNFSDANWATAQTARSGLIFAAFVFWLFCFGMSRYSMYTERRL 379 Lambda K H 0.329 0.142 0.471 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: 416 Number of extensions: 15 Number of successful extensions: 4 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: 396 Length of database: 385 Length adjustment: 31 Effective length of query: 365 Effective length of database: 354 Effective search space: 129210 Effective search space used: 129210 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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