Align MFS transporter (characterized, see rationale)
to candidate CCNA_01576 CCNA_01576 major facilitator superfamily transporter
Query= uniprot:A0A166QG26 (467 letters) >FitnessBrowser__Caulo:CCNA_01576 Length = 431 Score = 378 bits (970), Expect = e-109 Identities = 193/455 (42%), Positives = 269/455 (59%), Gaps = 47/455 (10%) Query: 14 QAVGNYRWTICALLFFATTVNYLDRQVLSLLAPDLSTQFGWSNSDYANIASVFQFVYAIS 73 + +G YRW I LLF A +NY+DRQ + L DLS +FGWS DYAN+ FQ YA++ Sbjct: 18 EKIGRYRWIIVTLLFLAMVINYVDRQTIGFLKHDLSVEFGWSEHDYANLVFYFQLSYAVA 77 Query: 74 MLFAGRVVDKIGTKTAYVVAICIWSTGAVMHAFAVPMGEGIGAVSSALGIAMIPVSIAGF 133 L G+V+DKIG + + +A IW + HA A + GF Sbjct: 78 YLVWGKVMDKIGARWGFGIAFLIWQVAHIAHAGAR--------------------GLTGF 117 Query: 134 MVSRAVLAIGEAGNFPIAIKATAEYFPKKERSFATGIFNSGANVGAILAPICVPLIASLW 193 + +R L +GEAG FP IKA E+FPKKER+FATGIFN+G N+GAI+ P+ VP I W Sbjct: 118 IFARMALGVGEAGGFPGGIKAVTEWFPKKERAFATGIFNAGTNIGAIVTPLVVPAIVLAW 177 Query: 194 GWEAAFIVIGMLGFVWVGVWIALYEKPEQQKRLSAQELAYIRSDQVVPVVTRPVPGVADK 253 GW+ AFIV G+ G +W+ +W+ +Y P + K LSA ELA+I D PV + Sbjct: 178 GWQMAFIVTGVAGLIWLPIWLLVYRTPRETKNLSAAELAHIEQDPADPV----------E 227 Query: 254 KVSWFKLLTYRQTWAFAFGKFMTDGVWWFFLFWLPTYLSAQYGMKGQAIVMPLAVLYSMT 313 K++W KLLT R+TWA+A GKF+ D +WW FLFWLP +L +YG+ + P+ +Y ++ Sbjct: 228 KIAWTKLLTKRETWAYAIGKFLIDPIWWMFLFWLPDFLGKRYGLDLKTFGPPIVAIYLLS 287 Query: 314 MIGSIGGGWFPSYFMSRGDAPYDGRMKAMLVIAFFPLLVLLAQPLGYISF----WVPVLL 369 GS+GGGW S FM G + R ML+ A LLA P+ + SF WV VL+ Sbjct: 288 DAGSVGGGWLSSNFMKMGWSINRARKITMLICA------LLAVPVMFASFADSLWVAVLI 341 Query: 370 IGVGASAHQAWSCNIFTTVSDMFPQKSIASVVGIGGLAGGLGGVVMTKIGGWVIDHYKLI 429 IGV +AHQ +S N++T SD+FP+ ++ SVVGIGG+ G +GG+V +K G V++ I Sbjct: 342 IGVATAAHQGFSANLYTLPSDVFPRGAVGSVVGIGGMLGAVGGMVFSKYIGGVLES---I 398 Query: 430 GDIHTGYMIMFAICALAYLVAWSVMKALVPRHKEI 464 G Y +F + AYL+A V+ L P+ + + Sbjct: 399 GT----YTPIFIVAGSAYLLALLVVHLLTPKMEPV 429 Lambda K H 0.327 0.140 0.449 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: 721 Number of extensions: 32 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: 467 Length of database: 431 Length adjustment: 33 Effective length of query: 434 Effective length of database: 398 Effective search space: 172732 Effective search space used: 172732 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