Align N-acetylglucosamine transporter nagP (characterized)
to candidate CA265_RS08575 CA265_RS08575 L-fucose:H+ symporter permease
Query= reanno::ANA3:7025962 (432 letters) >FitnessBrowser__Pedo557:CA265_RS08575 Length = 422 Score = 176 bits (447), Expect = 9e-49 Identities = 132/438 (30%), Positives = 204/438 (46%), Gaps = 32/438 (7%) Query: 4 DKSQQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTF 63 D S K LP +V +LFF+ G A L+ L+P+LK+ LN Q++LI S + A Sbjct: 6 DSSSGKKYLLPFILVISLFFLWGMAHNLDSILIPHLKKACNLNNRQSTLIDTSVFFAYFL 65 Query: 64 TALPSAWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQT 123 A+P+ +++K GYK M G+ LF+PAA + FL A ++G G T+L+T Sbjct: 66 MAIPAGMILKKWGYKATMISGLLAFAFGAFLFVPAANNLSYITFLIALFIIGCGLTMLET 125 Query: 124 AVNPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQV---- 179 + NPY LG A +R+++ N A ++AP++ IL S K L + Sbjct: 126 SANPYAAVLGDPAKATSRLNLAASFNGLAAMVAPMIGGLFIL-SGKSHTKEELAAMTDAG 184 Query: 180 ---QIDEMANSLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHP 236 E A S+ PY+ + I + V+A LPE+ + E KG AL H Sbjct: 185 RNSYFLEEAASVKTPYITLGIVLLVIAAIFYFIHLPEIKTKSIDGE--AKGSFFGALRHK 242 Query: 237 NLAFGVIALFVYVAVEVIAGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGII---LI 293 +L + V+A F YV +V A G SY + +L +T+G I Sbjct: 243 HLKWAVVAQFFYVGAQVCVTSFFIRMAQQGGGFDEKTAASYLAIYGLL-FTVGRFAGTAI 301 Query: 294 PRFISQPTALMISAILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLA 353 +F+S L I A++ +LL L + G SY + + +G Sbjct: 302 LQFVSSHKLLAIYAVISILLCLVAILG-KGSYVV-----------------YALGAIGFF 343 Query: 354 NAIVWPAVWPLALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVML 413 +I++P ++ L + G+G T GS+ LIM I GGA P G Q GY + L Sbjct: 344 MSIMFPTIFALGIDGIGDDTKPGSSWLIMSIVGGAILPFGMGSLIDMYGDNIQIGYSIPL 403 Query: 414 PCYLFILFYAVKGHKMRH 431 C+L IL++ ++G+K+ H Sbjct: 404 VCFLVILYFGLRGYKIAH 421 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: 506 Number of extensions: 27 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: 422 Length adjustment: 32 Effective length of query: 400 Effective length of database: 390 Effective search space: 156000 Effective search space used: 156000 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