Align Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized)
to candidate WP_044620926.1 H744_RS02965 PTS fructose transporter subunit IIC
Query= TCDB::Q5V5X5 (383 letters) >NCBI__GCF_000940995.1:WP_044620926.1 Length = 373 Score = 206 bits (524), Expect = 9e-58 Identities = 118/355 (33%), Positives = 194/355 (54%), Gaps = 32/355 (9%) Query: 20 TSVKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGW----------FLAQ 69 T VK +MTGVS+M+P + G + + +A IG + +N F A Sbjct: 15 TEVKTAIMTGVSYMLPLIIAGAVIMGIA-RIGASFYGIDNIWDGSHAEAANAVVRLFHAF 73 Query: 70 IGVAGL--TIMVPILGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAG 127 G GL ++M+P++ GYIA++IAD+PG+APG V G+ E G Sbjct: 74 DGFGGLALSLMLPVVAGYIAFSIADKPGIAPGM-----------------VAGLLAKEMG 116 Query: 128 AGYLGAIVAGLLAGYVARFF-KNLDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVA 186 G+LGA+ AG +AGY+ + + +P+ + P+ +IPV + +M++++G P+A Sbjct: 117 TGFLGALAAGFIAGYIVKLLVTKVKLPKSVASAGPIFIIPVGGTLLACLVMMYIIGDPLA 176 Query: 187 LANEGLTSFLQSMQGGQAIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPMAAV 246 N GL ++L M G IV+ ++GGM+ FD+GGP+NK A A ++ IY P A Sbjct: 177 AMNRGLENWLLGMSDGNKIVLAAVVGGMVGFDLGGPINKAAVTTAMAMLASGIYDPNTAA 236 Query: 247 MIGGMIPPIGLALSNFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAI 306 + +IPPIG+ ++ I ++ + + GK+ ++GL ++EGAIP+A A+P ++I Sbjct: 237 QVAIIIPPIGIGVATLIWKQRFPHSLQDAGKASTLMGLIGVSEGAIPFALANP-KIIVVN 295 Query: 307 VAGSAVGGATSMALGVTMPAPHGGIFVVLLSNQPLAFLGSILLGSLVTAVVATVI 361 V GSAVG A ++ LG AP G + L L ++ +I +GS + AV + ++ Sbjct: 296 VIGSAVGSALAVGLGAVNRAPISGFYGWLAVENWLVYVLAIAVGSGIIAVGSLLV 350 Lambda K H 0.322 0.139 0.399 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: 541 Number of extensions: 35 Number of successful extensions: 4 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: 383 Length of database: 373 Length adjustment: 30 Effective length of query: 353 Effective length of database: 343 Effective search space: 121079 Effective search space used: 121079 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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