Align Hexuronate transporter (characterized)
to candidate CCNA_01039 CCNA_01039 putative hexuronate transporter, major facilitator superfamily
Query= SwissProt::P0AA78 (432 letters) >FitnessBrowser__Caulo:CCNA_01039 Length = 438 Score = 434 bits (1117), Expect = e-126 Identities = 210/417 (50%), Positives = 291/417 (69%), Gaps = 3/417 (0%) Query: 1 MRKIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTV 60 M K+K LRW++I LVTLG V+ YLTR+T+ AAPTL++EL IS +YS+I +A+ + Sbjct: 19 MPKLKALRWWIIGLVTLGAVINYLTRSTMGVAAPTLLKELGISVTEYSWITSAFQLGI-M 77 Query: 61 MQPVAGYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGL 120 +QP+ GYVLD LG + G+A+FAV W++ A LA SW G AV RG +G AE + PAG+ Sbjct: 78 LQPICGYVLDTLGLRTGFAVFAVAWSLIAMAHGLANSWQGFAVLRGFLGLAEGSAQPAGM 137 Query: 121 KASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMA 180 K + WFPAKER A G FN+G+SIG+++APPLVVWA+++ +W+ AF+++G + +W + Sbjct: 138 KTVAIWFPAKERGFAGGVFNIGASIGSVLAPPLVVWAVLVWNWRAAFVLTGVMGLVWVVL 197 Query: 181 WLIFYKHPRDQKHLTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALPRFLAE 240 WL FY+ P +TDEER I GQEA H + A + S+ IL+ QFWGIALPRFLA+ Sbjct: 198 WLAFYRSPEKHPSMTDEERAVIAAGQEA-HLEAVAARPSILSILKQGQFWGIALPRFLAD 256 Query: 241 PAWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLIV 300 P WGT W+PL++ + GF+LK+IA+FAWMP + ADLGC+ G + LF + GV LI Sbjct: 257 PTWGTLAFWVPLYLSQTRGFDLKQIALFAWMPFVAADLGCMAGPVI-ALFLQKRGVTLIN 315 Query: 301 SRKMVVTLGAVLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRNEVA 360 +R++ TLGAVLM G +G + Y AI LLC+GGFAHQ LS +IT++SD+F RNEVA Sbjct: 316 ARRIAFTLGAVLMTGMMFVGKVESAYAAIALLCLGGFAHQTLSVTVITMASDLFRRNEVA 375 Query: 361 TANGLTGMSAWLASTLFALVVGALADTIGFSPLFAVLAVFDLLGALVIWTVLQNKPA 417 T GL GM L LF+L++G L +G+ P F L V D+LGA+++WT++++ A Sbjct: 376 TVAGLAGMMGNLGLLLFSLLIGGLVAKVGYDPFFIALGVLDILGAILLWTLVKDPAA 432 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: 655 Number of extensions: 34 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: 438 Length adjustment: 32 Effective length of query: 400 Effective length of database: 406 Effective search space: 162400 Effective search space used: 162400 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