Align PTS system lactose-specific EIICB component; EIICB-Lac; EII-Lac; EC 2.7.1.207 (characterized)
to candidate WP_038018222.1 HA49_RS13180 PTS sugar transporter subunit IIC
Query= SwissProt::P23531 (568 letters) >NCBI__GCF_000757425.2:WP_038018222.1 Length = 428 Score = 245 bits (626), Expect = 2e-69 Identities = 136/421 (32%), Positives = 230/421 (54%), Gaps = 21/421 (4%) Query: 13 PFFEKISRNIYLRAIRDGFIAGMPVILFSSIFILIAYVP----------NAWGFHWSKDI 62 P KIS ++ AIRDGFIA MP ++ S ++ AY P W + + + Sbjct: 16 PVAAKISSQRHIMAIRDGFIAVMPFMIIGSFILIFAYPPFSEDNQFFIARGW-LYIAAEY 74 Query: 63 ETFLMTPYSYSMGILAFFVGGTTAKALTDSKNRDLPATNQINFLSTMLASMVGFLLMAAE 122 + L+TPY+ +MGI++ ++ + L ++ L+T L ++V FLL+ Sbjct: 75 KQQLLTPYNMTMGIMSVYICPAISYCLARHY--------RLEGLNTALLALVAFLLICC- 125 Query: 123 PAKEGGFLTAFMGTKGLLTAFIAAFVTVNVYKVCVKNNVTIRMPEDVPPNISQVFKDLIP 182 P G ++++G G+ TA I A + + +V + N+ IR+PE VP NI + F LIP Sbjct: 126 PLNNGTMESSYLGGSGIFTAIIVAVLVCELSRVLHQKNIGIRLPEQVPDNIRKSFNQLIP 185 Query: 183 FTVSVVLLYGLELLVKGTLGVTVAESIGTLIAPLFSAADGYLGITLIFGAYAFFWFVGIH 242 ++ +++L+ + L V+ G+ + ++I L +PL SA+D + + WF GIH Sbjct: 186 LSLVLLILFPVSLAVQSLSGMLIPQAIMALFSPLLSASDSLPAVIIAVIICHVLWFAGIH 245 Query: 243 GPSIVEPAIAAITYANIDVNLHLIQAGQHADKVITSGTQMFIATMGGTGATLIVPFLFMW 302 G +IV + A N+ +N + +G A+ + F T+GG+GATL + L++ Sbjct: 246 GATIVSGFLQAFWLTNLGINQSKLASGLPAEHIFVEPFWAFFITLGGSGATLGLVLLYL- 304 Query: 303 ICKSDRNRAIGRASVVPTFFGVNEPILFGAPIVLNPIFFVPFIFAPIVNVWIFKFFVDTL 362 KS R+IG+ S+VP+ F +NEP++FG+PIV+N +FF+PFI P+VN + F + Sbjct: 305 RSKSAHLRSIGKISLVPSLFNINEPVIFGSPIVMNTLFFIPFILTPVVNAVLAWFAIKYG 364 Query: 363 NMNSFSANLPWVTPGPLGIVLGTNFQVLSFILAGLLVVVDTIIYYPFVKVYDEQILEEER 422 + + PW +PGP+G T + + + +L +LV +IYYPF K+Y+ +L EE+ Sbjct: 365 LVAHIVSLAPWTSPGPIGAAWATGWDINAALLVLVLVCSSALIYYPFCKLYERSLLAEEQ 424 Query: 423 S 423 + Sbjct: 425 N 425 Lambda K H 0.324 0.140 0.414 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: 572 Number of extensions: 26 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: 568 Length of database: 428 Length adjustment: 34 Effective length of query: 534 Effective length of database: 394 Effective search space: 210396 Effective search space used: 210396 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 (21.5 bits) S2: 52 (24.6 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