Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate PP_1299 PP_1299 putative amino acid ABC transporter - membrane subunit
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__Putida:PP_1299 Length = 365 Score = 243 bits (619), Expect = 8e-69 Identities = 143/379 (37%), Positives = 214/379 (56%), Gaps = 40/379 (10%) Query: 4 LTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWATTKAQWAVIQVNLRLFLVGRFPQT 63 L W+R NLFS+W N+LLT+ L +V ++ WA A W R T Sbjct: 20 LAWMRANLFSSWLNTLLTLFAIYLVWLIVPPLLQWALIDANWVGTT---------RADCT 70 Query: 64 EYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGLFAFIVGLLLILFTLDLSSRLWLLL 123 + W+ + G G + +L WR +DL+ L +L Sbjct: 71 KEGACWVF--VQQRFGQFMYGYY--PTELRWR-----------------VDLTVWLAVLG 109 Query: 124 TAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILWLI--GGGFGLRPVSSNLWNGLLLT 181 A L I F + + L +L+ +P++ + + GG GL V ++ W GL+LT Sbjct: 110 AAPLFIKRFPRKA--------FYGLGFLVLYPVLAYTLLHGGYLGLESVPTSQWGGLMLT 161 Query: 182 LLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVMLPLFF 241 L++A + IV + P+G+LLALGR S +P V+ + +IE RGVPLI +LF++ VMLPLF Sbjct: 162 LVIATVGIVGALPLGILLALGRRSRMPAVKVVCVTFIEFWRGVPLITVLFMSSVMLPLFL 221 Query: 242 AADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTFFVVLLIVLP 301 + D++LRA+ G++LF +AY+AE VRGGLQA+ +GQ EAA A+GL + + L++LP Sbjct: 222 PEGMSFDKLLRAMIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILP 281 Query: 302 QALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAEVYLFIGLIY 361 QAL+ VIP +V FI LFKDTSL+ ++GL +L + A P ++G E Y+F L++ Sbjct: 282 QALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPAWLGMATEGYVFAALVF 341 Query: 362 WLFCYSMSLASRRLERQLN 380 W+FC+ MS S LER+L+ Sbjct: 342 WIFCFGMSRYSMHLERKLD 360 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: 504 Number of extensions: 24 Number of successful extensions: 4 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: 365 Length adjustment: 30 Effective length of query: 351 Effective length of database: 335 Effective search space: 117585 Effective search space used: 117585 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