Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate N515DRAFT_3134 N515DRAFT_3134 multiple sugar transport system permease protein
Query= uniprot:D4GP36 (317 letters) >FitnessBrowser__Dyella79:N515DRAFT_3134 Length = 292 Score = 122 bits (305), Expect = 1e-32 Identities = 84/270 (31%), Positives = 134/270 (49%), Gaps = 16/270 (5%) Query: 40 GIPFVLMSIAVYGGTGYNFAISFTDYEGLGTPDYSTLD---LEMYAQALSSDAFIAAAQN 96 G+ F+L IA A+S TDY+ D L L Y + L F +A + Sbjct: 19 GLFFLLPVIAA-------LALSLTDYDLYALADIRDLRFVALGNYWELLHRPLFWSALGH 71 Query: 97 NLVLLVGFTTICLVLGLFLAILLDHGI-RFSEKFQTVYLLPMSLSFVVTAQLWLWMFNVE 155 L ++ + +V L A+LL+ + R F+T P+ + V A +W ++FN + Sbjct: 72 TLYFVLVGVPLSIVASLGAALLLNSPLARCKPLFRTALFAPVVTTVVAVAVIWRYLFNTK 131 Query: 156 SGILNLVVTTLGFNPVDWLGNPSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQFEAA 215 G+ N + LG +PVDWLG+P A+ +IL +W+ GY M+++LA LQ+IP D +EAA Sbjct: 132 YGLANYALGGLGIHPVDWLGDPRWAMPTIILFAVWKNFGYNMIIFLAALQAIPADLYEAA 191 Query: 216 RVDGASITRTYLRIIVPQLKEASVSAAVVLM--VFALKAFTFLYALVGRYRPPNGTDILA 273 R+DGAS R + I +P L + ++ + F L A F+ G P T + Sbjct: 192 RIDGASPLRQFRHITLPMLGPTLLMVGILTVSGYFQLFAEPFVMTEGG---PLQSTTSVL 248 Query: 274 TLMVRRAFKFGEWAYSAAIATMLLIMALGV 303 LM FK+ ++A+A +L ++ V Sbjct: 249 YLMYEEGFKWWNLGSASAVAFLLFLIMFAV 278 Lambda K H 0.326 0.140 0.424 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: 265 Number of extensions: 10 Number of successful extensions: 1 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: 317 Length of database: 292 Length adjustment: 27 Effective length of query: 290 Effective length of database: 265 Effective search space: 76850 Effective search space used: 76850 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: 48 (23.1 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