Align Hexuronate transporter (characterized)
to candidate AZOBR_RS23835 AZOBR_RS23835 hexuronate transporter ExuT
Query= SwissProt::P0AA78 (432 letters) >FitnessBrowser__azobra:AZOBR_RS23835 Length = 428 Score = 432 bits (1110), Expect = e-125 Identities = 202/412 (49%), Positives = 284/412 (68%), Gaps = 4/412 (0%) Query: 1 MRKIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTV 60 M+ ++GLRW ++AL+ LGT++ Y+ RNT+ AP L EEL+ +T+QYSYI++ + Y++ Sbjct: 1 MKIVRGLRWKVLALIMLGTIINYIDRNTLGILAPMLKEELHFTTEQYSYIVSVFQLCYSL 60 Query: 61 MQPVAGYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGL 120 MQP+AGYV D++G K GYAMFA +W A +G W +A RG +G +EAA +P+G Sbjct: 61 MQPIAGYVTDLIGLKFGYAMFAFVWGSAAALHAFSGGWQSMAFFRGLLGISEAAAMPSGA 120 Query: 121 KASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMA 180 K ++ WFPAKERSIA G+FN GSS+GAMIAPPLV+W V SWQ+AF+++G L +M Sbjct: 121 KTAALWFPAKERSIATGWFNTGSSVGAMIAPPLVIWLSVTWSWQVAFVVTGMLGVGLSML 180 Query: 181 WLIFYKHPRDQKHLTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALPRFLAE 240 WL Y++P + LT EE YI++GQE QV K S+ +++ R+FWGIA RFL E Sbjct: 181 WLALYRNPENHPRLTKEEHAYILDGQE---QVQLPKP-SMKRVVTMRKFWGIAAARFLTE 236 Query: 241 PAWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLIV 300 PAW TF+ WIPL+M G ++K+ A+FAW+P LFAD+GC+L GYL P F + F ++L+ Sbjct: 237 PAWQTFSFWIPLYMVSTRGMDIKQFALFAWLPFLFADIGCVLSGYLSPFFAKRFRMSLVN 296 Query: 301 SRKMVVTLGAVLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRNEVA 360 SR + +GAV MIGP +IGL ++P AI L +G FAHQ LS L L +D F + +VA Sbjct: 297 SRIAGIGIGAVCMIGPALIGLTSSPITAIFLFSVGAFAHQMLSSLLYALVTDTFEKQDVA 356 Query: 361 TANGLTGMSAWLASTLFALVVGALADTIGFSPLFAVLAVFDLLGALVIWTVL 412 TA G GM+ ++ +F+L++G LA TIG+ PLF L+VFD+ +V+ VL Sbjct: 357 TATGFGGMAGYMGGMIFSLIIGQLASTIGYEPLFVCLSVFDITAFIVVLVVL 408 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: 639 Number of extensions: 29 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: 428 Length adjustment: 32 Effective length of query: 400 Effective length of database: 396 Effective search space: 158400 Effective search space used: 158400 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