Align Hexuronate transporter (characterized)
to candidate WP_057508172.1 ABB28_RS08240 MFS transporter
Query= SwissProt::P0AA78 (432 letters) >NCBI__GCF_001431535.1:WP_057508172.1 Length = 436 Score = 245 bits (625), Expect = 2e-69 Identities = 132/418 (31%), Positives = 233/418 (55%), Gaps = 12/418 (2%) Query: 1 MRKI---KGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAA 57 +RK+ +RW ++ L+ + TV+ Y+ RN +A P + E+ + Y+ ++ + Sbjct: 10 LRKVPVRSAVRWLIVGLIAVATVINYIDRNALAVMWPEIAREVGATKDDYALLVTVFMLF 69 Query: 58 YTVMQPVAGYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIP 117 Y Q + G + D++GT++G+A+ +W++ A+ S ++ R +G +EA P Sbjct: 70 YAAGQFLFGRLFDLIGTRMGFALSISVWSLSIALHAVTHSILSFSLVRAMLGVSEAGAWP 129 Query: 118 AGLKASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIW 177 +KA++EWFPA+ER++A G FN G+SIGA+++ P + + W+ F++ G + F+W Sbjct: 130 GAVKANAEWFPARERALAQGVFNAGASIGAIVSAPAIAALYLWLGWRGTFVLVGVMGFLW 189 Query: 178 AMAWLIFYKHPRDQKH--LTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALP 235 + WL Y+ D KH ++D ER I+ Q A A + SV ++L +RQ WG+ Sbjct: 190 LLPWLFVYRAGPD-KHPWVSDAERRLIMEDQ-AGAADPAAPRRSVRELLAHRQSWGMLAC 247 Query: 236 RFLAEPAWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFG 295 RFL +P W F +W+P+++ + +GF++K+I +FAW+P + A LG + GG+L R G Sbjct: 248 RFLLDPIWWLFVSWLPIYLAETFGFDIKQIGLFAWVPFVGAMLGSLTGGWLSGRLIR-AG 306 Query: 296 VNLIVSRKMVVTLGAVLMIGPGMIG--LFTNPYVAIMLLCIGGFAHQALSGALITLSSDV 353 ++ +RK +TLG V+M P ++G L P A++ + F Q G + TL D+ Sbjct: 307 HSVDRARKWSITLGCVVM-APALLGAVLAAEPLTAVLTIAAVLFGFQVAIGNIQTLPGDL 365 Query: 354 FGRNEVATANGLTGMSAWLASTLFALVVGALADTIGFSPLFAVLAVFDLLGALVIWTV 411 FG V T GL G++A +A TL + + ++P+F ++A L + +W + Sbjct: 366 FGGRSVGTLAGLGGLAA-VAGTLITTWLVPVLTRESYAPMFMLVAALVPLSLIALWWI 422 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: 667 Number of extensions: 35 Number of successful extensions: 2 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: 436 Length adjustment: 32 Effective length of query: 400 Effective length of database: 404 Effective search space: 161600 Effective search space used: 161600 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 24 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