Align D-Gluconate:H+ symporter of 448 aas and 11 TMSs (characterized)
to candidate 18320 b4296 KpLE2 phage-like element; predicted transporter (NCBI)
Query= TCDB::P12012 (448 letters) >FitnessBrowser__Keio:18320 Length = 449 Score = 538 bits (1385), Expect = e-157 Identities = 268/450 (59%), Positives = 348/450 (77%), Gaps = 3/450 (0%) Query: 1 MPLIIVALGILALLFLIMGLKLNTFISLLVVSFGVALALGMPFDKVVSSIEAGIGGTLGH 60 MPLIIV GI LL L + +KLNTF+SL++VS VA+A GM KVV+S+E+G+GGTLGH Sbjct: 1 MPLIIVVAGIALLLLLTIKIKLNTFVSLIIVSIAVAIASGMDLSKVVTSVESGLGGTLGH 60 Query: 61 IALIFGLGAMLGKLIADSGGAQRIAMTLVNKFGEKNIQWAVVIASFIIGIALFFEVGLVL 120 I LIFG G MLG+L+AD+GGAQRIA+T++N FG+ + WAVV ++FI+GIALFFEVGL+L Sbjct: 61 IGLIFGFGVMLGRLLADAGGAQRIALTMLNYFGKNKLDWAVVCSAFIVGIALFFEVGLIL 120 Query: 121 LIPIVFAISRELKISILFLGIPMVAALSVTHGFLPPHPGPTAIAGEYGANIGEVLLYGFI 180 L+PI+FAI+RE KIS +F+ +PM++ L V HGFLPPHPGPT IA EYGA++G VL+YG I Sbjct: 121 LVPILFAIAREAKISPMFMCVPMLSGLLVAHGFLPPHPGPTVIAREYGADVGLVLIYGII 180 Query: 181 VAVPTVLIAGPLFTKFAKKIVPASFAKNGNIASLGTQKTFNLEETPGFGISVFTAMLPII 240 V +PT ++ GP+ KF ++I+P +F K GNIASLG + F+ E PGFGIS TAMLP+I Sbjct: 181 VGIPTFILCGPVLNKFCQRIIPDAFKKEGNIASLGATRRFSESEMPGFGISFLTAMLPVI 240 Query: 241 IMSVATIIDLLQETIGFADNGVL-AFIRLIGNASTAMIISLLVAVYTMGIKRNIPVKTVM 299 +M+V TII + AD+G+ I +GN++ AM+ISLL A+YTMG+ R + +M Sbjct: 241 LMAVVTIIQMTHAK-SAADSGLFYNVILFLGNSTIAMLISLLFAIYTMGLGRGKTIPDLM 299 Query: 300 DSCSTAISQIGMMLLIIGGGGAFKQVLINGGVGDYVADLFKGTALSPIILAWLIAAILRI 359 DSC AI+ I +LLIIGGGGAFKQVLI+ GVG Y++ L G ++PI++AW +AA LRI Sbjct: 300 DSCGKAIAGIAGLLLIIGGGGAFKQVLIDSGVGQYISTLVSGMDINPILMAWGVAAFLRI 359 Query: 360 SLGSATVAALSTTGLVIPLLG-HSDVNLALVVLATGAGSVIASHVNDAGFWMFKEYFGLS 418 LGSATVAA+ST GLVIPLL H + NLAL+ LATGAGS I SHVNDA FWM K++FGL+ Sbjct: 360 CLGSATVAAISTAGLVIPLLAVHPNTNLALITLATGAGSCICSHVNDASFWMIKDFFGLT 419 Query: 419 MKETFATWTLLETIISVAGLGFILLLSLVV 448 KET +WTL+ T++S++GL FILL SLV+ Sbjct: 420 TKETLLSWTLMSTLLSISGLIFILLASLVL 449 Lambda K H 0.327 0.144 0.411 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: 650 Number of extensions: 22 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: 448 Length of database: 449 Length adjustment: 33 Effective length of query: 415 Effective length of database: 416 Effective search space: 172640 Effective search space used: 172640 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