Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 3606890 Dshi_0320 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__Dino:3606890 Length = 432 Score = 216 bits (550), Expect = 1e-60 Identities = 139/408 (34%), Positives = 219/408 (53%), Gaps = 41/408 (10%) Query: 4 LTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVW-------------------ATTKAQ 44 + WLR NLF + +S+LT++ +A WL ++ W Sbjct: 29 VNWLRSNLFYSIPSSILTLLTAAFIYWLSSILMPWMFNGVWDANSIRDCREILDGAIGGC 88 Query: 45 WAVIQVNLRLFLVGRFPQTEYWRVWIVLAIASTLGAVTAGIFFN-QQKLTWRKVGLFAFI 103 +AVI + G +P EYWR VLA A+ +FF +K+ W GLF FI Sbjct: 89 FAVIAERWPQLIFGNYPNEEYWRA--VLAFVGLFVALAPVLFFKLPRKMLWF-TGLFPFI 145 Query: 104 VGLLLILFTLDLSSRLWLLLTAVL-LIPGFLLGSRLTN------LVAPWLS--LIWLLSF 154 + L W+ + A++ ++ G++ L +VA + L W+ Sbjct: 146 A------YWLIWGGSAWVSVMALVGVVVGYVAFKALEERSFFGAIVAALFATLLFWIFIS 199 Query: 155 PIILWLIGG--GFGLRPVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRW 212 P+ + + L V S G ++ ++ I LS P+G+ LALGR SNLP+++ Sbjct: 200 PLAVNALSSVVALSLPQVESRFIGGFMINFILGTSGIALSLPLGIALALGRQSNLPIIKG 259 Query: 213 FSILYIEIVRGVPLIGILFLAQVMLPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGG 272 +++IE +RGVPLI +LF+A VML F D VLR I + LF++AY+AE +RGG Sbjct: 260 VCVVFIEFIRGVPLITLLFVASVMLAYFLPPGTSFDLVLRVIIMITLFASAYIAEAIRGG 319 Query: 273 LQAVSRGQVEAAKALGLNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVE 332 L A+ RGQ EA +LGL+ + + LI+LPQAL+ IP++V IGLFKDT+L+S++ + + Sbjct: 320 LAALPRGQYEAGDSLGLDYWQSMRLIILPQALKISIPSIVNIAIGLFKDTTLVSIISMFD 379 Query: 333 LTGIARS-ILAQPQFIGRYAEVYLFIGLIYWLFCYSMSLASRRLERQL 379 + G+ + IL+ ++ G Y E+ F G+++++FCY +S S+ LERQL Sbjct: 380 MLGMIQGPILSSTEWFGVYWELLGFAGVLFFVFCYGISQYSQWLERQL 427 Lambda K H 0.332 0.145 0.452 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: 578 Number of extensions: 32 Number of successful extensions: 5 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: 381 Length of database: 432 Length adjustment: 31 Effective length of query: 350 Effective length of database: 401 Effective search space: 140350 Effective search space used: 140350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 50 (23.9 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