Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF2296 PGA1_c23280 amino acid transport sytem, permease protein
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Phaeo:GFF2296 Length = 664 Score = 188 bits (477), Expect = 3e-52 Identities = 100/233 (42%), Positives = 144/233 (61%), Gaps = 1/233 (0%) Query: 44 EWILRGLPWWLVILAFMALACRSSRRWSLTLAVCALLETVGVLGIWDLTMQTLALMLMAT 103 E +L W V A +AL R W L A + V G WD M TLA +L+A Sbjct: 106 EALLPAASWIAVTAAVIALG-HYCRNWGLAAVAGACFAYLAVFGQWDSAMVTLASVLIAV 164 Query: 104 IVSVVIGVPMGILVAKSRVVRNITLPVLDVMQTMPSFVYLIPALMLFGLGKVPAILATII 163 + G+ GI + V I P+LD+MQT+P F YL+P L +FG G V A++ATII Sbjct: 165 PIGAGGGLLTGIWAYRHPVGERILSPLLDLMQTIPIFAYLVPILFMFGFGPVSALVATII 224 Query: 164 YAVPPLIRLTDLGIRQVDAEVVEAATAFGGSPGQILFGVELPLATPTIMAGLNQTIMMAL 223 YA PP+IR+T L ++ VD E+++ G +P Q+++ V +P A+ ++M G+NQ IM+ L Sbjct: 225 YATPPMIRVTILALKSVDPEILDFGRMAGTTPRQLMWRVLVPSASQSLMVGVNQVIMLTL 284 Query: 224 SMVVVASMIGARGLGEQVLNGIQTLDVGKGLEAGIGIVILAVVLDRITQGFGK 276 +MV++ASMIGA GLG VL ++ LD+G G EAGI IV+LA+ +DR++Q F + Sbjct: 285 NMVIIASMIGAGGLGFDVLAALRRLDIGAGFEAGIAIVVLAIAVDRLSQAFAE 337 Score = 164 bits (415), Expect = 5e-45 Identities = 96/266 (36%), Positives = 152/266 (57%), Gaps = 20/266 (7%) Query: 15 NDFIQALVTNYGWVFKAISGVILKAVLFIEWI-------LRGLPW-WLVILAFMALACRS 66 ++ ++ L NY F+A+ V F+ W L G+PW W V + L Sbjct: 393 SETVKYLNVNYFDAFEAVK------VFFLHWFMLPIKKTLLGIPWPWAVAM----LTLVG 442 Query: 67 SRRWSLTLAV-CALLET-VGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVR 124 R L LA+ C + T + G+W M T+ L + I++ +IGVP+G+L A ++ Sbjct: 443 WRAGGLRLALMCGSMSTLIAFSGLWAKAMVTVYLCGASVILATLIGVPLGVLAALNKRAG 502 Query: 125 NITLPVLDVMQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEV 184 +D +QT+PSFVYLIP +MLF +G A++A ++YA+ P +R G+R V E+ Sbjct: 503 VAIGLFIDTLQTLPSFVYLIPVVMLFRVGDFTAMIAIVLYALAPAVRYAAHGMRSVSGEL 562 Query: 185 VEAATAFGGSPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNG 244 +EA G + Q+L V LP+A P I+ G+NQTIM+ALSM+V+ +++G R LG++V Sbjct: 563 IEAGLVSGCTRWQLLRMVRLPMALPEILLGINQTIMLALSMLVITALVGTRDLGQEVYIA 622 Query: 245 IQTLDVGKGLEAGIGIVILAVVLDRI 270 + D G+GL AG+ I +A++ DR+ Sbjct: 623 LTKADTGRGLVAGLAIAFIAIIADRL 648 Lambda K H 0.327 0.142 0.422 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: 540 Number of extensions: 24 Number of successful extensions: 3 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: 285 Length of database: 664 Length adjustment: 32 Effective length of query: 253 Effective length of database: 632 Effective search space: 159896 Effective search space used: 159896 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 (21.7 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