Align Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized)
to candidate Ga0059261_1891 Ga0059261_1891 MFS transporter, sugar porter (SP) family
Query= TCDB::A0QZX3 (498 letters) >FitnessBrowser__Korea:Ga0059261_1891 Length = 466 Score = 414 bits (1063), Expect = e-120 Identities = 215/451 (47%), Positives = 290/451 (64%), Gaps = 4/451 (0%) Query: 44 IAAVAALGGLLFGYDSAVINGAVDSIQEDFGIGNYALGLAVASALLGAAAGALSAGRIAD 103 I AVA +GGLLFGYDS +NG D ++ F + LG V S L+G GA AGR+AD Sbjct: 15 IVAVATIGGLLFGYDSGAVNGTQDGLKSAFALSEGGLGFTVGSLLIGCFIGAFLAGRLAD 74 Query: 104 RIGRIAVMKIAAVLFFISAFGTGFAPETVTLVVFRIVGGIGVGVASVIAPAYIAETSPPG 163 IGR VM + AVLF I A GF+ E V RI GG+ VG ASV++PAYI+E +P Sbjct: 75 LIGRRNVMILTAVLFLIGALIQGFSHEQWIFVAARIAGGMAVGAASVLSPAYISEVAPAN 134 Query: 164 IRGRLGSLQQLAIVLGIFTSFVVNWLLQWAAGGPNEVLAMGLDAWRWMFLAMAVPAVLYG 223 IRGR+ ++QQ+ I+ G+ +FVVN+ L AG + G +AWRWM+ A+PA ++ Sbjct: 135 IRGRMTTIQQIMIISGLTAAFVVNYWLAKTAGASTNLFWGGYEAWRWMYWMQAIPATVFL 194 Query: 224 ALAFTIPESPRYLVATHKIPEARRVLSMLLGQKNLEITITRIRDTLEREDKPSWRDLKKP 283 F IPESPRYLV+ + EA RVL+ L G +T I+ + + +P+ RD+ P Sbjct: 195 IALFFIPESPRYLVSKGRNAEATRVLTSLFGAGTATNKLTEIQASFS-DHRPTLRDILDP 253 Query: 284 T-GGIYGIVWVGLGLSIFQQFVGINVIFYYSNVLWQAVGFSADQSAIYTVITSVVNVLTT 342 GG+ IVW GL L++FQQ VGINVIFYY LWQ GF+ + + + +++ V++ Sbjct: 254 VKGGVRPIVWAGLLLAVFQQLVGINVIFYYGATLWQLAGFTENDALLINIVSGFVSIAAC 313 Query: 343 LIAIALIDKIGRKPLLLIGSSGMAVTLATMAVIFANATVKPDGTPDLPGASGLIALIAAN 402 + +AL+D+IGRKPLLLIGS+GMAV L M F+ ++ G L G+IA+IAAN Sbjct: 314 FVTVALVDRIGRKPLLLIGSAGMAVALFAMVFAFSRGSLDAQGKLVLSQQLGIIAVIAAN 373 Query: 403 LFVVAFGMSWGPVVWVLLGEMFPNRFRAAALGLAAAGQWAANWLITVSFPELRNHLGLA- 461 L+VV F +SWGPV+WV+LGEMFPN+ R +AL + QW +N+LI SFP + LGLA Sbjct: 374 LYVVFFNVSWGPVMWVMLGEMFPNQIRGSALAVCGFAQWFSNYLIAQSFPIMAAGLGLAV 433 Query: 462 -YGFYALCAVLSFLFVSKWVEETRGKNLEDM 491 Y FYA+CAV+SF VSK++ ET+G LEDM Sbjct: 434 SYSFYAVCAVISFFLVSKFIHETKGVELEDM 464 Lambda K H 0.324 0.140 0.421 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: 631 Number of extensions: 28 Number of successful extensions: 3 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: 498 Length of database: 466 Length adjustment: 34 Effective length of query: 464 Effective length of database: 432 Effective search space: 200448 Effective search space used: 200448 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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