Align N-acetylglucosamine transporter nagP (characterized)
to candidate WP_156804425.1 B3C1_RS01975 glucose/galactose MFS transporter
Query= reanno::ANA3:7025962 (432 letters) >NCBI__GCF_000299915.1:WP_156804425.1 Length = 421 Score = 409 bits (1051), Expect = e-119 Identities = 217/425 (51%), Positives = 284/425 (66%), Gaps = 12/425 (2%) Query: 15 MAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWVIRK 74 MAI+ LFFI GF TWLNGSL+P+LK + QLN FQA + F+FYIA T ALP A ++ + Sbjct: 1 MAIIGLLFFIFGFVTWLNGSLIPFLKIVCQLNDFQALFVAFAFYIAYTVMALPMAALLER 60 Query: 75 VGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQTAVNPYVVRLGP 134 +GY+NGMA G+ IM LLFIPAA + +GLFL A V+G+G TLLQTA NPYVV LGP Sbjct: 61 LGYRNGMAWGLAIMAAGALLFIPAALSAQYGLFLLALFVLGSGLTLLQTASNPYVVLLGP 120 Query: 135 EESAAARVSVMGILNKGAGVIAPLVFSALILDSFKD-------RIGTTLTQVQIDEMANS 187 ESAA R+S+MGI+NK AGV+ PL+F++L+L + + Q+D +A Sbjct: 121 AESAAMRISIMGIINKTAGVLVPLLFTSLVLSDLAQVNQASLAHLDPAVRDAQLDAVAER 180 Query: 188 LVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAFGVIALFV 247 LV PYL MA + L V+ SPLPE++ + E KG++ L +P L G + LF Sbjct: 181 LVLPYLYMAAALMALIALVRLSPLPEIAPQGE----GGKGRLAELLRYPQLILGALTLFA 236 Query: 248 YVAVEVIAGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGIILIPRFISQPTALMISA 307 +V +EVIA DTIG LGV + +TSYTMV MVLGY LG++LIPR++SQ AL+ S Sbjct: 237 FVGLEVIAADTIGLLGEKLGVARFASLTSYTMVFMVLGYGLGVVLIPRWLSQSRALLYSG 296 Query: 308 ILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWPAVWPLALS 367 + G+ LA+LF S A+++ L +PD +LF+A +GLA+A+VWPAVWPLAL Sbjct: 297 LAGVAAVLAVLFSSPGSQALSSFLWGWTPIPTVPDPVLFVALMGLAHALVWPAVWPLALD 356 Query: 368 GLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYLFILFYAVKGH 427 GLG+ T+ GSALLIMGIAGGA PL +G + + QQ Y++ LPCYL I FYA+KGH Sbjct: 357 GLGRHTAQGSALLIMGIAGGALLPLAFGHLAESLGSIQQ-AYVLALPCYLLIAFYALKGH 415 Query: 428 KMRHW 432 +MR W Sbjct: 416 RMRRW 420 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: 630 Number of extensions: 35 Number of successful extensions: 5 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: 421 Length adjustment: 32 Effective length of query: 400 Effective length of database: 389 Effective search space: 155600 Effective search space used: 155600 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 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