Align PTS system, IID component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex (characterized)
to candidate 17213 b3140 N-acetylgalactosamine-specific enzyme IID component of PTS (NCBI)
Query= TCDB::Q82ZC6 (290 letters) >FitnessBrowser__Keio:17213 Length = 263 Score = 105 bits (262), Expect = 1e-27 Identities = 92/281 (32%), Positives = 143/281 (50%), Gaps = 30/281 (10%) Query: 19 EITNKDVTKAYLRWHFANEIPHSFERYLAPSLLYAMMPLLKKLYKDDEQ-LKAAYMRQLL 77 EI+ KD+T+ R + ++ER A +AM+P+LKK+YKDD+ L AA L Sbjct: 4 EISKKDITRLGFRSSLL-QASFNYERMQAGGFTWAMLPILKKIYKDDKPGLSAAMKDNLE 62 Query: 78 FFNTQLSWGGGVITGLMASMEQERAKEEHEGREIMMQDDLMYNTKAGLMGALAGIGDAID 137 F NT + G + GL+ SME E+ E R D + K L G +AGIGDAI Sbjct: 63 FINTHPNLVG-FLMGLLISME-----EKGENR------DTIKGLKVALFGPIAGIGDAIF 110 Query: 138 SGTVQYIFIAIAVPWAQQGSALGAIFPFVAFALYQVLLGVFFARQSFKMGRNATGLMQSA 197 T+ I I +A QG+ LG P + FA+Y L +FF R + + G+ Sbjct: 111 WFTLLPIMAGICSSFASQGNLLG---PILFFAVY---LLIFFLRVGWTHVGYSVGVKAID 164 Query: 198 GIQKAIEML----SVLGLFMMGILAGNYVKVSSTLQFKLSGREFVV--QDILDQIVPGLL 251 +++ +M+ ++LG+ ++G L +YV ++ F + V QD D++ P +L Sbjct: 165 KVRENSQMIARSATILGITVIGGLIASYVHINVVTSFAIDNTHSVALQQDFFDKVFPNIL 224 Query: 252 PLAVVMGVYWFY-TKKGLKVTQALLWLTGIL-IVLATVGIL 290 P+A + +Y+F KK V L+ +T +L IV + GIL Sbjct: 225 PMAYTLLMYYFLRVKKAHPV--LLIGVTFVLSIVCSAFGIL 263 Lambda K H 0.324 0.138 0.402 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: 208 Number of extensions: 14 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: 290 Length of database: 263 Length adjustment: 25 Effective length of query: 265 Effective length of database: 238 Effective search space: 63070 Effective search space used: 63070 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: 41 (22.0 bits) S2: 47 (22.7 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