Align N-acetylglucosamine porter, NagP (characterized)
to candidate WP_011373691.1 SUDEN_RS10795 glucose/galactose MFS transporter
Query= TCDB::Q8EBL0 (435 letters) >NCBI__GCF_000012965.1:WP_011373691.1 Length = 426 Score = 409 bits (1051), Expect = e-119 Identities = 211/424 (49%), Positives = 294/424 (69%), Gaps = 7/424 (1%) Query: 9 KSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPS 68 KSSF+PM I+ LFFI GF TWLNGSL+P+LK + +LN F+A + F+FYI+ T ALP Sbjct: 4 KSSFIPMFIMGTLFFIFGFVTWLNGSLIPFLKIVCELNEFEALFVTFAFYISYTVMALPM 63 Query: 69 AWVIRKVGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVNPY 128 A+V+ K GYK+GMALG+GVM I LLFIPAA++ F +FL A +G G T+LQ+A NPY Sbjct: 64 AYVLEKTGYKDGMALGLGVMAIGALLFIPAAQSAEFIIFLIALFTLGTGLTILQSASNPY 123 Query: 129 VVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDEMANGL 188 +V LGP ESAA R+S+MGI+NKGAGV+AP+VFSAL+ ++ +++ + +A L Sbjct: 124 IVYLGPVESAAMRISIMGIINKGAGVLAPIVFSALLFLDVGEQ--DVMSEASREILAQKL 181 Query: 189 VLPYLGMAVFIGILALAVKKSPLPELSNEDEVADHTDKSQIKAALSHPNLALGVLALFVY 248 ++PY+ MA+ + L + +K S L L+ +D+ +++KS I P L LG +ALF Y Sbjct: 182 IVPYIVMALILVALIVLIKFSSLESLTIKDD-KSNSEKSSI---FEFPRLILGAIALFFY 237 Query: 249 VAVEVIAGDTIGTFALSLGIDHYGVMTSYTMVCMVLGYILGILLIPRVISQPTALMISAI 308 V +EVIAGDTI +A S+G++ Y +TS+TM MVLGYI GI+ IPR +SQ AL+ SA+ Sbjct: 238 VGIEVIAGDTIALYAQSIGVESYSTLTSFTMFFMVLGYIAGIVFIPRYLSQKNALIGSAL 297 Query: 309 LGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGLANAIVWPAVWPLALSG 368 G+L LG++F + S+ ++ +L G LPDT+ +A LG ANA+VWP++WPLAL+G Sbjct: 298 FGILFLLGVVFSLSTSHLLSEILWGWSGVRTLPDTITFVALLGFANALVWPSIWPLALNG 357 Query: 369 MGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVMLPCYLFILFYAVKGHK 428 +GK T GSALLIM IAGGA P+ +G ++ Q Y++ + Y FIL+YAV GHK Sbjct: 358 LGKHTPKGSALLIMSIAGGALLPLLFGKIAQLVS-SMQTAYLLGIVSYAFILYYAVAGHK 416 Query: 429 MRSW 432 + SW Sbjct: 417 ISSW 420 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: 708 Number of extensions: 37 Number of successful extensions: 3 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: 426 Length adjustment: 32 Effective length of query: 403 Effective length of database: 394 Effective search space: 158782 Effective search space used: 158782 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 24 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