Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 8502448 DvMF_3154 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__Miya:8502448 Length = 229 Score = 132 bits (331), Expect = 1e-35 Identities = 76/207 (36%), Positives = 130/207 (62%), Gaps = 12/207 (5%) Query: 177 GLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVM 236 GL +++++A I +F +G+ L R S+ +R +I+Y+EI+RG+PL+ ++F Sbjct: 25 GLAMSVVLAIGGIFGAFWLGLGFGLLRLSDRWWLRLPAIIYVEIIRGIPLLMLIFW---- 80 Query: 237 LPLFFAADVRLDRVL----RAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTF 292 +F A + L R L A+ ++F+ AY+AE VR G+ A+ GQ+EAA+ GL+ Sbjct: 81 --FYFLAPIVLGRTLPEAESALVAFIVFTGAYIAEIVRAGVLALPHGQMEAARGTGLSKS 138 Query: 293 FVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAE 352 ++ ++LPQALR +IP+ V QF+ L KDTSL ++G+ ELT A I + + AE Sbjct: 139 QAMIYVILPQALRNMIPSFVNQFVSLTKDTSLAYIIGVSELTRTATQI--NNRELTAPAE 196 Query: 353 VYLFIGLIYWLFCYSMSLASRRLERQL 379 ++ I ++Y++ C++++ ASRR+ERQ+ Sbjct: 197 LFFTIAVLYFIVCWTLTAASRRMERQM 223 Score = 30.0 bits (66), Expect = 7e-05 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 10/78 (12%) Query: 44 QWAVIQVNLRLFLVGRFPQTEY--WRVWIVLAIASTLGAVTAGIFFNQQKLT---WRKVG 98 QW V+ N LVG +PQ + +VLAI GA G+ F +L+ W ++ Sbjct: 2 QWDVVWRNFDYLLVGSWPQGPLGGLAMSVVLAIGGIFGAFWLGLGFGLLRLSDRWWLRLP 61 Query: 99 LFAFI-----VGLLLILF 111 ++ + LL+++F Sbjct: 62 AIIYVEIIRGIPLLMLIF 79 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: 312 Number of extensions: 20 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: 381 Length of database: 229 Length adjustment: 26 Effective length of query: 355 Effective length of database: 203 Effective search space: 72065 Effective search space used: 72065 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: 48 (23.1 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