Align Galactofuranose-binding protein YtfQ (characterized)
to candidate SM_b21345 SM_b21345 sugar uptake ABC transporter substrate-binding protein precursor
Query= SwissProt::P39325 (318 letters) >FitnessBrowser__Smeli:SM_b21345 Length = 327 Score = 221 bits (562), Expect = 2e-62 Identities = 131/301 (43%), Positives = 174/301 (57%), Gaps = 8/301 (2%) Query: 13 AAMSSMALAAPLTVGFSQVGSESGWRAAETNVAKSEAEKRGITLKIADGQQKQENQIKAV 72 A + +A VGF+Q S + WR A+TN K+EAEK G L D Q+ V Sbjct: 28 AELPKLAQKETYKVGFAQTESNNPWRIAQTNSMKAEAEKLGHQLVYTDAAGSAAKQVADV 87 Query: 73 RSFVAQGVDAIFIAPVVATGWEPVLKEAKDAEIPVFLLDRSID---VKDKSLYMTTVTAD 129 S +AQGVD IF+AP P + AK A IPV LLDRS+D K Y+T + +D Sbjct: 88 NSMIAQGVDLIFLAPREEKPLIPAVMAAKKAGIPVILLDRSVDPSLAKAGEDYVTFIGSD 147 Query: 130 NILEGKLIGDWLVKEVNGKPCNVVELQGTVGASVAIDRKKGFAEAIKNAPNIKIIRSQSG 189 I EGK I +WLVK NGK ++EL+GT G+S A DRKKGF E IK A +I+ SQSG Sbjct: 148 FIEEGKRIAEWLVKNANGK-SKIIELEGTTGSSPANDRKKGFDETIKAAGGFEIVASQSG 206 Query: 190 DFTRSKGKEVMESFIKAENNGKNICMVYAHNDDMVIGAIQAIKEAGLKPGKDILTGSIDG 249 DF R KG++V E+ ++A + +VYAHND+M IGAI AI+ AG PGKD+L SIDG Sbjct: 207 DFARDKGRQVAEALLQAHPDAD---IVYAHNDEMAIGAIAAIEAAGKVPGKDVLVLSIDG 263 Query: 250 VPDIYKAMMDGEANASVELTPNMAGPAFDALEKYKKDGTMPEKLTLTKSTLYLPDTAKEE 309 + +A++DG+ A VE P AF+ + +Y K G + + + + Y A E Sbjct: 264 GKEAVQAVIDGKIAAVVECNPRFGPKAFETMLRYAK-GEKIDPMVINEDKFYDSSNAAAE 322 Query: 310 L 310 L Sbjct: 323 L 323 Lambda K H 0.313 0.130 0.363 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: 267 Number of extensions: 15 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: 318 Length of database: 327 Length adjustment: 28 Effective length of query: 290 Effective length of database: 299 Effective search space: 86710 Effective search space used: 86710 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 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