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) >FitnessBrowser__Phaeo:GFF1918 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:
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