Align N-acetylglucosamine porter, NagP (characterized)
to candidate WP_057509309.1 ABB28_RS14540 glucose/galactose MFS transporter
Query= TCDB::Q8EBL0 (435 letters) >NCBI__GCF_001431535.1:WP_057509309.1 Length = 429 Score = 310 bits (793), Expect = 7e-89 Identities = 175/425 (41%), Positives = 259/425 (60%), Gaps = 31/425 (7%) Query: 15 MAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWVIRK 74 +AIV LFF++GF TWLNG L+ ++K +L+ A L+L FY++ F ALPS+W++R+ Sbjct: 17 IAIVGVLFFLIGFFTWLNGPLITFVKLAFELDEVGAFLVLMVFYLSYFFLALPSSWILRR 76 Query: 75 VGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVNPYVVRLGP 134 G K G++L + VM F A + + L ++G+G LLQTA+NPY+ LGP Sbjct: 77 TGMKKGLSLSLLVMAAGAATFGEFATQRWYPGALGGLFIIGSGLALLQTAINPYISILGP 136 Query: 135 EESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQI-------DEMANG 187 E+AA R+++MGI NK AG++AP++ L+L D + T + Q + ++ A Sbjct: 137 IETAARRIALMGICNKVAGMLAPVLIGTLVLHGVGD-LSTAVEQADVATRAALLNDFAAK 195 Query: 188 LVLPYLGMAVFIGILALAVKKSPLPELSNEDEVADHTDKSQIK--AALSHPNLALGVLAL 245 + PYLGMA + +L++AV SPLPEL + + A K I+ + P+L LGVL L Sbjct: 196 IHAPYLGMAALLVVLSVAVLFSPLPELKSSEANAAPAGKGGIERSSIFQFPHLWLGVLCL 255 Query: 246 FVYVAVEVIAGDTIGTF--ALSLGIDHYGVMTSYTMVCMVLGYILGILLIPRVISQPTAL 303 FVYV VEV+AGD IGT+ L +D + TS T+ M++GY++G+LLIPR +SQ L Sbjct: 256 FVYVGVEVMAGDAIGTYGHGFDLPLDQTKMFTSLTLGAMLVGYVVGLLLIPRFVSQSRYL 315 Query: 304 MISAILGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGLANAIVWPAVWP 363 ISA LG+L +G F + Y ++ +A LG ANA++WPA++P Sbjct: 316 SISASLGVLFCVGAYF--THGYV----------------SVAFVALLGFANAMMWPAIFP 357 Query: 364 LALSGMGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVMLPCYLFILFYA 423 LA+ G+G+ T TGSALL+MGIAGGA P ++ ++ D Q ++M+PCYL+ILFY+ Sbjct: 358 LAIRGLGRFTETGSALLVMGIAGGAIIPQAFAVLKQHVDF-QLVFLLLMVPCYLYILFYS 416 Query: 424 VKGHK 428 GH+ Sbjct: 417 TIGHR 421 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: 599 Number of extensions: 38 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: 429 Length adjustment: 32 Effective length of query: 403 Effective length of database: 397 Effective search space: 159991 Effective search space used: 159991 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