Align N-acetylglucosamine transporter nagP (characterized)
to candidate Echvi_0508 Echvi_0508 L-fucose:H+ symporter permease
Query= reanno::ANA3:7025962 (432 letters) >FitnessBrowser__Cola:Echvi_0508 Length = 431 Score = 174 bits (441), Expect = 5e-48 Identities = 130/431 (30%), Positives = 217/431 (50%), Gaps = 34/431 (7%) Query: 9 KSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPS 68 K++ P ++ +LF + G A + +L+ K+IL + Q S I +FY A ALP+ Sbjct: 12 KATLWPFILLTSLFLLWGLANNMTDTLLAAFKKILSMTDTQTSFIQLAFYGAYFCLALPA 71 Query: 69 AWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQTAVNPY 128 A I+K YK+G+ LG+G+ + GLLF PA+ T +G FL A V+ G ++L+T+ NPY Sbjct: 72 AIYIKKYTYKSGVLLGLGLFAVGGLLFYPASITMSYGFFLFALYVLAGGLSILETSANPY 131 Query: 129 VVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFK-----DRIGTTLTQVQ--I 181 ++ +GPE SA R+++ N +I ++ IL +R T Q+Q Sbjct: 132 IMVMGPEASATRRLNLAQSFNPVGSIIGVVLSKFFILSKLNVAEADERSRMTAEQLQQVR 191 Query: 182 DEMANSLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAFG 241 E ++++ Y+G+A+F+ V+ + +K + +P S E + + G +K L + N FG Sbjct: 192 QEELDAVMGTYVGVALFLVVMWVLIKFTKMPTAS-EGGLQDSLGNG-LKRLLGNKNYVFG 249 Query: 242 VIALFVYVAVEV-IAGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGIIL---IPRFI 297 V+A F YV ++ I TI + L + ++Y + +VL +T+ L + +F+ Sbjct: 250 VLAQFFYVGAQIGIWSYTIRYVMMELDMNESDA-SNYYLAAIVL-FTVSRFLFTALMKFV 307 Query: 298 SQPTALMISAILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIV 357 + ISAI + LT+ ++FG +IA LV G +++ Sbjct: 308 RPSLLMAISAIGAIGLTMVVIFGHGMVGSIA---LVCISG---------------CMSLM 349 Query: 358 WPAVWPLALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYL 417 +P ++ LA GLG T G + LIM I GGA P GL S + D + V CYL Sbjct: 350 FPTIYGLAAEGLGDDTKLGGSGLIMAILGGAIFPFIQGLVSDSLD-SIHLSFFVPAACYL 408 Query: 418 FILFYAVKGHK 428 ++ Y + +K Sbjct: 409 VVVAYGLFHYK 419 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: 486 Number of extensions: 25 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: 431 Length adjustment: 32 Effective length of query: 400 Effective length of database: 399 Effective search space: 159600 Effective search space used: 159600 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