Align Glucose-binding protein aka TT_C0328, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate GFF1918 PGA1_c19500 putative sugar-binding periplasmic protein
Query= TCDB::Q72KX2 (414 letters) >lcl|FitnessBrowser__Phaeo:GFF1918 PGA1_c19500 putative sugar-binding periplasmic protein Length = 414 Score = 143 bits (361), Expect = 8e-39 Identities = 105/350 (30%), Positives = 166/350 (47%), Gaps = 19/350 (5%) Query: 15 SALAQGGKLEIFSWWAGDEGPALEALIRLYKQKYP--GVEVINATVTGGAGVNARAVLKT 72 +A A G + E+ WW G A A I+++ Y G E I+ + GG A+ Sbjct: 19 AATADGIRAEVIHWWVS-AGEA--AAIKVFADAYTANGGEWIDNGIGGGG---AKTTFVN 72 Query: 73 RMLGGDPPDTFQVHAGMELIGTWVVANRMEDLSALFRQEGWLQAFPKGLIDLISYKGGIW 132 R++GGD P Q + E V A + L A W FP + +++ G + Sbjct: 73 RLMGGDAPQVGQFNTSREFEEI-VDAGLLHSLDAEAEAGNWSALFPGIIDNVVKRDGSYY 131 Query: 133 SVPVNIHRSNVMWYLPAKLKEWGVNPPRTWDEFLATCQTLKQKGLEAPLAL-GENWTQQH 191 +VPVNIH SN +W+ + + G++ P WD F +TLK+ G+ PLA+ GE W ++ Sbjct: 132 AVPVNIHGSNWLWHNNQVMADAGLDVPTDWDSFFEAAETLKEAGI-IPLAVGGEAWQERL 190 Query: 192 LWESVALAVLGPDDWNNLWNGK--LKFTDPKAVRAWEVFGRVLDCANK---DAAGLSWQQ 246 + SV L+V G D + L+ K T + ++V+ R+ + + G SW Sbjct: 191 TFNSVLLSVGGQDLYLRLFEEKDTTALTSDEMKEVFDVYSRLRTLVRETDPGSPGRSWND 250 Query: 247 AVDRVVQGKAAFNVMGDWAAGYMTTTLKLKPGTDFAWAPSPGTQGVFMMLSDSFGLPK-- 304 A + V+ G+AA +MGDWA G + + PG ++ P+ +M+ D F PK Sbjct: 251 ATNMVITGQAAMQIMGDWAKGEFLSA-GMTPGVEYGCTPAVIAGSPYMISGDVFVFPKTG 309 Query: 305 GAKNRQNAINWLRLVGSKEGQDTFNPLKGSIAARLDSDPSKYNAYGQSAM 354 ++R+ + E Q FN +KGSI R D D S+ + GQ A+ Sbjct: 310 NEEDREAQSLMATTMLDAEVQVAFNNIKGSIPVRPDVDTSQLDVCGQQAI 359 Lambda K H 0.319 0.134 0.429 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: 512 Number of extensions: 27 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: 414 Length of database: 414 Length adjustment: 31 Effective length of query: 383 Effective length of database: 383 Effective search space: 146689 Effective search space used: 146689 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 (21.8 bits) S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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