Align N-acetylglucosamine porter, NagP (characterized)
to candidate 7025545 Shewana3_2696 major facilitator transporter (RefSeq)
Query= TCDB::Q8EBL0 (435 letters) >FitnessBrowser__ANA3:7025545 Length = 452 Score = 416 bits (1069), Expect = e-121 Identities = 226/431 (52%), Positives = 296/431 (68%), Gaps = 16/431 (3%) Query: 9 KSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPS 68 + SF+PM ++ LFF+ GF TWLNG+L+P+LK QLN F+A L+ F FYIA ALP+ Sbjct: 15 QGSFIPMLLIGILFFVFGFVTWLNGALIPFLKIACQLNEFEAYLVTFVFYIAYFVMALPT 74 Query: 69 AWVIRKVGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVNPY 128 + ++ ++GYK GM LG+G+M LFI AA FA FL A V+G G TLLQTA NPY Sbjct: 75 SSILTRLGYKMGMTLGLGIMAAGAGLFIVAALVGHFATFLLALFVLGTGLTLLQTAANPY 134 Query: 129 VVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLT-------QVQI 181 +V +GP ESAA R+S+MGI+NKGAG I P++F+A IL + T L Q+ + Sbjct: 135 IVCIGPRESAAMRISLMGIVNKGAGFIVPIIFTAWILTGMEPYSETALASLSEAQRQLAL 194 Query: 182 DEMANGLVLPYLGMA-VFIGILALAVKKSPLPELSNEDEVADHTDKSQI--KAALSHPNL 238 E+AN LV PYL M V +G++A V SPLPE E+ + +++Q KA L +P + Sbjct: 195 TELANRLVHPYLMMMLVLLGLMAF-VWFSPLPE----PELGERVERTQTDWKAILQYPQV 249 Query: 239 ALGVLALFVYVAVEVIAGDTIGTFALSLGIDHYGVMTSYTMVCMVLGYILGILLIPRVIS 298 LG L LF YV EVIAGD+IG F+ LG+ H+G+MTSYTM MVLGY+LGILLIPR IS Sbjct: 250 ILGALTLFCYVGAEVIAGDSIGLFSQGLGVAHFGMMTSYTMGFMVLGYVLGILLIPRWIS 309 Query: 299 QPTALMISAILGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGLANAIVW 358 Q TAL+ SAI GLL TLG+L D+ S A++ LLL G + +PD +L +A LGLANA+VW Sbjct: 310 QQTALVGSAIAGLLFTLGVLLSDSQSQALSELLLGWLGVLPVPDPVLYLALLGLANALVW 369 Query: 359 PAVWPLALSGMGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVMLPCYLF 418 PAVWPLAL G+G+LT+T SALLIMGIAGGA P+ +G ++ + Q Y ++LPCY Sbjct: 370 PAVWPLALEGLGRLTATASALLIMGIAGGAILPLLYGYIAHSQGDSQM-AYFLLLPCYGL 428 Query: 419 ILFYAVKGHKM 429 I +YA+ GHK+ Sbjct: 429 IFYYAIWGHKL 439 Lambda K H 0.326 0.141 0.414 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: 771 Number of extensions: 35 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: 435 Length of database: 452 Length adjustment: 32 Effective length of query: 403 Effective length of database: 420 Effective search space: 169260 Effective search space used: 169260 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 (21.6 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