Align N-acetylglucosamine porter, NagP (characterized)
to candidate WP_009133853.1 HMPREF9450_RS05320 sugar MFS transporter
Query= TCDB::Q8EBL0 (435 letters) >NCBI__GCF_000231275.1:WP_009133853.1 Length = 445 Score = 289 bits (739), Expect = 1e-82 Identities = 157/443 (35%), Positives = 265/443 (59%), Gaps = 27/443 (6%) Query: 8 QKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALP 67 +K+S MAI+ +FFI GF +W+N L+PY K +LN FQ+ LI+F+ Y A A+P Sbjct: 13 RKTSVAAMAILGLMFFIFGFTSWVNSILVPYFKIGCELNHFQSYLIVFALYSAYLIMAIP 72 Query: 68 SAWVIRKVGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVNP 127 S+ ++++VG+K G+ G + L+FIPAA + + +FL V+GAG +LQ A NP Sbjct: 73 SSAILKRVGFKRGIMYGFFCTALGALIFIPAAWWRSYPVFLAGSFVIGAGSAMLQAAANP 132 Query: 128 YVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALIL-----DSFKDRIGTTL----TQ 178 YV +GP + R+++MGI NK AG++APL+F+A++L D F TL Sbjct: 133 YVTMIGPINTTVKRMAIMGICNKFAGLVAPLIFAAVVLKVTDSDLFVQLESATLDPAARS 192 Query: 179 VQIDEMANGLVLPYLGMAVFIGILALAVKKSPLPELS----NEDEVADHTDKSQIKAALS 234 +D + + +++PY A F+ ++ + ++ S LPEL+ N+ EVA + + Sbjct: 193 AMLDSLVHRVMVPYAIFAAFLIVIGVFIRFSMLPELNLEEKNKQEVAPGGEGK--TSVFQ 250 Query: 235 HPNLALGVLALFVYVAVEVIAGDTIGTFALSLGIDHYGVMT--SYTMVCMVLGYILGILL 292 P L LGV+A+F+++ +V+ DTI ++A ++G+D T SYT+ ++LG +LG+LL Sbjct: 251 FPYLILGVVAMFLHIGTQVVTIDTIISYAQTMGMDLLEAKTFPSYTLSLVILGNVLGVLL 310 Query: 293 IPRVISQPTALMISAILGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGL 352 IP++ISQ I LG LL+LG+++G+ V F G ++ + +GL Sbjct: 311 IPKIISQTRVFQICCTLGFLLSLGVVWGNTQ---------VDFLGHHANISIWFLVGIGL 361 Query: 353 ANAIVWPAVWPLALSGMGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVM 412 AN++V+ +WPLA+ G+G+ T TGS++LIM + G A P+ +G ++ + + + ++ Sbjct: 362 ANSLVYGGIWPLAIRGLGRFTKTGSSMLIMALFGNAVVPLIYGYIADTASL-RIAYFWIL 420 Query: 413 LPCYLFILFYAVKGHKMRSWSAK 435 LP + +++FYA G+++ SWS + Sbjct: 421 LPGFAYLMFYAFCGYRITSWSGR 443 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: 643 Number of extensions: 46 Number of successful extensions: 6 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: 445 Length adjustment: 32 Effective length of query: 403 Effective length of database: 413 Effective search space: 166439 Effective search space used: 166439 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