Align neutral amino acid transporter A (characterized)
to candidate GFF2732 HP15_2676 proton/sodium-glutamate symport protein
Query= CharProtDB::CH_091534 (532 letters) >FitnessBrowser__Marino:GFF2732 Length = 426 Score = 184 bits (467), Expect = 6e-51 Identities = 120/435 (27%), Positives = 219/435 (50%), Gaps = 41/435 (9%) Query: 51 GVLAGAGLGAALRGLSLSRTQV---TYLAFPGEMLLRMLRMIILPLVVCSLVSG-AASLD 106 G++ G LG ++ GL T +LAFPG++ L ++MI++PLV+ S+V G AA D Sbjct: 16 GLITGTLLGPSV-GLVEPETGTLIGNWLAFPGQLFLATIQMIVIPLVIASVVRGLAAGED 74 Query: 107 ASCLGRLGGIAVAYFGLTTLSASALAVALAFIIKPGSGAQTLQSSDLGLEDSGPPPVPKE 166 L +LG +F +TT A+++ + + +I PG L + + ++ P Sbjct: 75 LEQLRKLGLRVTGFFVITTAMAASIGLWIGDLINPGRMMAGL-GTPVAAGENSVPVASMP 133 Query: 167 TVDSFLDLARNLFPSNLVVAAFRTYATDYKVVTQNSSSGNVTHEKIPIGTEIEGMNILGL 226 VD L P N P+ +EG +L + Sbjct: 134 GVDELPKTLIGLLPGN------------------------------PLDAMVEGQ-MLQV 162 Query: 227 VLFALVLGVALKKLGSE-GEDLIRFFNSLNEATMVLVSWIMWYVPVGIMFLVGSKIVEMK 285 V+F++++G+AL + E ++ +SL + M +V W M P+ + L+ + Sbjct: 163 VIFSIIVGIALVSMAPEKSRPMLDLLDSLQQICMTVVRWAMRLAPIAVFGLMAQLTTTLG 222 Query: 286 DIIVLVTSLGKYIFASILGHVIHGGIVLPLIYFVFTRKNPFRFLLGLLAPFATAFATCSS 345 +L + Y+ I G ++ G+ + LI + ++P RFL AF+T SS Sbjct: 223 FRAML--GMASYVATVIAGLLVLLGVYM-LILKLLAGQSPVRFLKDTRDVLLLAFSTSSS 279 Query: 346 SATLPSMMKCIEENNGVDKRISRFILPIGATVNMDGAAIFQCVAAVFIAQLNNVELNAGQ 405 +A +P ++ E+ GV +S+F++P+GAT+NM+G A++Q VA +F+AQ+ ++L+ G Sbjct: 280 AAVMPLSIRTAEDKLGVRPSVSQFVIPLGATINMNGTALYQAVATIFLAQVYGIDLSMGS 339 Query: 406 IFTILVTATASSVGAAGVPAGGVLTIAIILEAIGLPTHDLPLILAVDWIVDRTTTVVNVE 465 + ++ A +S+G+ P G++ +A++L+ +G+P + LI+ VD I+D T +NV Sbjct: 340 MALVVAMAVGASIGSPATPGVGIVILAMVLQTVGIPPSGIALIMGVDRILDMCRTAINVT 399 Query: 466 GDALGAGILHHLNQK 480 GD + ++ +L K Sbjct: 400 GDLVTCRLMENLAGK 414 Lambda K H 0.320 0.136 0.390 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: 410 Number of extensions: 22 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: 532 Length of database: 426 Length adjustment: 33 Effective length of query: 499 Effective length of database: 393 Effective search space: 196107 Effective search space used: 196107 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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