Align N-acetylglucosamine transporter nagP (characterized)
to candidate CA265_RS08675 CA265_RS08675 glucose/galactose MFS transporter
Query= reanno::ANA3:7025962 (432 letters) >FitnessBrowser__Pedo557:CA265_RS08675 Length = 428 Score = 337 bits (864), Expect = 4e-97 Identities = 185/437 (42%), Positives = 273/437 (62%), Gaps = 33/437 (7%) Query: 5 KSQQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFT 64 KS Q P+ I+ ALFFI GF TW NG+L+P+ K L+ QA + F+ Y+A F Sbjct: 6 KSGQTQGPKPLIIICALFFIFGFVTWANGTLIPFFKLSFGLSNLQAFFVTFASYMAYFFL 65 Query: 65 ALPSAWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQTA 124 ALPS+W+++KVG+KNG+ LG+ I+ L L+FIPAA+T+ FGLFL V G LLQTA Sbjct: 66 ALPSSWILKKVGFKNGIVLGLVILGLGSLIFIPAAQTRTFGLFLTGIFVQGAALALLQTA 125 Query: 125 VNPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDS-------FKDRIGTTLT 177 NPY+ +GP ESAA R+S+ GI NK AG+I PL+ +L L + K G Sbjct: 126 SNPYLTIIGPIESAAKRISIAGICNKFAGMIVPLIMGSLFLKNASEVEKQIKAATGAVHE 185 Query: 178 QVQIDEMANSLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQI---KAALS 234 Q+ ++++ + PY+ +AI + A+ +K + LPE+ E++V + + KG++ K+ Sbjct: 186 QL-LNDVLGRVNMPYIVLAIVFCLFAIFIKFTNLPEVEVEEDVIDES-KGEVVKHKSIFQ 243 Query: 235 HPNLAFGVIALFVYVAVEVIAGDTIGTFALSLGV--EHYGVMTSYTMVCMVLGYTLGIIL 292 P+L G + +FVYV EV+AGD IG + LG+ E G +TS T+ M++GY +GI+ Sbjct: 244 FPHLFLGALCIFVYVGAEVMAGDIIGIYGRELGISPEISGKLTSITLFSMLIGYIIGIVT 303 Query: 293 IPRFISQPTALMISAILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGL 352 IP++ISQ AL I AILG++ T+ S+ I++ V +F+A LGL Sbjct: 304 IPKYISQQKALRICAILGIIFTIL-------SFVISSWFAV-----------IFVALLGL 345 Query: 353 ANAIVWPAVWPLALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMV- 411 AN+++WPA++PL +S LGK T GSA++IMGIAGGA PL + + + Q Y++ Sbjct: 346 ANSLMWPAIFPLGISHLGKFTKIGSAIMIMGIAGGALMPLLYAFLNEKLHVNFQLAYLLT 405 Query: 412 MLPCYLFILFYAVKGHK 428 +LPCYL+IL++A+KGHK Sbjct: 406 VLPCYLYILYFAIKGHK 422 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: 604 Number of extensions: 34 Number of successful extensions: 7 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: 428 Length adjustment: 32 Effective length of query: 400 Effective length of database: 396 Effective search space: 158400 Effective search space used: 158400 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