Align N-acetylglucosamine transporter nagP (characterized)
to candidate 5208608 Shew_1119 glucose/galactose transporter (RefSeq)
Query= reanno::ANA3:7025962 (432 letters) >FitnessBrowser__PV4:5208608 Length = 418 Score = 728 bits (1878), Expect = 0.0 Identities = 370/418 (88%), Positives = 388/418 (92%), Gaps = 1/418 (0%) Query: 15 MAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWVIRK 74 MAIVA LFFILGFATWLNGSLMPYLKQILQL P QASLILFSFYIAVTFTALPSAWVIRK Sbjct: 1 MAIVAGLFFILGFATWLNGSLMPYLKQILQLTPLQASLILFSFYIAVTFTALPSAWVIRK 60 Query: 75 VGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQTAVNPYVVRLGP 134 VGYK GMA+GMGIMM+AGLLFIPAAKTQ+F LFL AQLVMGTGQTLLQTAVNPYVVR+GP Sbjct: 61 VGYKTGMAMGMGIMMIAGLLFIPAAKTQVFALFLFAQLVMGTGQTLLQTAVNPYVVRIGP 120 Query: 135 EESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDEMANSLVFPYLG 194 EESAAARVSVMGILNKGAGVIAPLVF+ALILDSFKDR+G LTQ QIDEMAN LVFPYLG Sbjct: 121 EESAAARVSVMGILNKGAGVIAPLVFTALILDSFKDRVGVELTQAQIDEMANGLVFPYLG 180 Query: 195 MAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAFGVIALFVYVAVEVI 254 MAIFIGVLAL VKKSPLPEL NEDE E T KG + ALSHPNLA GV+ALF YVAVEVI Sbjct: 181 MAIFIGVLALLVKKSPLPELENEDEQEEGT-KGHTREALSHPNLALGVVALFFYVAVEVI 239 Query: 255 AGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGIILIPRFISQPTALMISAILGLLLT 314 AGDTIGTFALSLGVE+YGVMTSYTM+CMV+GY+LGI+ IPRFISQP ALMISAILGL+LT Sbjct: 240 AGDTIGTFALSLGVENYGVMTSYTMICMVIGYSLGILTIPRFISQPKALMISAILGLMLT 299 Query: 315 LAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWPAVWPLALSGLGKLTS 374 L ILFGDN SYAIANALLVPFGG LPDTLL IAFLGLANAIVWPAVWPLALSG+GKLTS Sbjct: 300 LGILFGDNESYAIANALLVPFGGAMLPDTLLMIAFLGLANAIVWPAVWPLALSGMGKLTS 359 Query: 375 TGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYLFILFYAVKGHKMRHW 432 TGSALL+MGIAGGAFGPLFWGLTSSAT +GQQGGYMVMLPCYLFILFYAVKG+KMR W Sbjct: 360 TGSALLVMGIAGGAFGPLFWGLTSSATSLGQQGGYMVMLPCYLFILFYAVKGYKMRSW 417 Lambda K H 0.327 0.141 0.421 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: 839 Number of extensions: 38 Number of successful extensions: 2 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: 432 Length of database: 418 Length adjustment: 32 Effective length of query: 400 Effective length of database: 386 Effective search space: 154400 Effective search space used: 154400 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