Align Hexuronate transporter (characterized)
to candidate CCNA_01576 CCNA_01576 major facilitator superfamily transporter
Query= SwissProt::P0AA78 (432 letters) >FitnessBrowser__Caulo:CCNA_01576 Length = 431 Score = 231 bits (590), Expect = 3e-65 Identities = 136/408 (33%), Positives = 217/408 (53%), Gaps = 9/408 (2%) Query: 3 KIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTVMQ 62 KI RW ++ L+ L V+ Y+ R T+ L E S Y+ ++ + +Y V Sbjct: 19 KIGRYRWIIVTLLFLAMVINYVDRQTIGFLKHDLSVEFGWSEHDYANLVFYFQLSYAVAY 78 Query: 63 PVAGYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGLKA 122 V G V+D +G + G+ + ++W V A A A G AR A+G EA P G+KA Sbjct: 79 LVWGKVMDKIGARWGFGIAFLIWQVAHIAHAGARGLTGFIFARMALGVGEAGGFPGGIKA 138 Query: 123 SSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMAWL 182 +EWFP KER+ A G FN G++IGA++ P +V ++ WQMAFI++G IW WL Sbjct: 139 VTEWFPKKERAFATGIFNAGTNIGAIVTPLVVPAIVLAWGWQMAFIVTGVAGLIWLPIWL 198 Query: 183 IFYKHPRDQKHLTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALPRFLAEPA 242 + Y+ PR+ K+L+ E +I Q +K++ ++L R+ W A+ +FL +P Sbjct: 199 LVYRTPRETKNLSAAELAHI-----EQDPADPVEKIAWTKLLTKRETWAYAIGKFLIDPI 253 Query: 243 WGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLIVSR 302 W F W+P F+ K YG +LK L +D G + GG+L F + G ++ +R Sbjct: 254 WWMFLFWLPDFLGKRYGLDLKTFGPPIVAIYLLSDAGSVGGGWLSSNFMK-MGWSINRAR 312 Query: 303 KMVVTLGAVLMIGPGMIGLFTNP-YVAIMLLCIGGFAHQALSGALITLSSDVFGRNEVAT 361 K+ + + A+L + P M F + +VA++++ + AHQ S L TL SDVF R V + Sbjct: 313 KITMLICALLAV-PVMFASFADSLWVAVLIIGVATAAHQGFSANLYTLPSDVFPRGAVGS 371 Query: 362 ANGLTGMSAWLASTLFALVVGALADTIG-FSPLFAVLAVFDLLGALVI 408 G+ GM + +F+ +G + ++IG ++P+F V LL LV+ Sbjct: 372 VVGIGGMLGAVGGMVFSKYIGGVLESIGTYTPIFIVAGSAYLLALLVV 419 Lambda K H 0.326 0.138 0.437 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: 635 Number of extensions: 46 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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