Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate SMa2309 SMa2309 ABC transporter permease
Query= TCDB::Q72KX4 (268 letters) >FitnessBrowser__Smeli:SMa2309 Length = 273 Score = 169 bits (427), Expect = 8e-47 Identities = 91/256 (35%), Positives = 150/256 (58%), Gaps = 4/256 (1%) Query: 17 FLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEAFRPK---FQNSVVLAVSA 73 +L P++ V+LT+ + A + +W WP TA P F NS+V+ + + Sbjct: 18 WLAPLFAVILTSFRSMADVMSGNLWGWPTEIAVVENYTAVFTQTPMAGYFLNSLVITIPS 77 Query: 74 TLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMKSIGLYGSLFG 133 + + +L G+VLA++ F G+ ++FAL + G F+P+Q ++IP+ M + LY + Sbjct: 78 VIGVLSLSTLAGFVLARYRFPGNMVIFALFVGGNFLPHQIMMIPVRDLMVRLNLYDTTTA 137 Query: 134 LVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPLSVPAFVVVAI 193 L++ HV + TL RN+ + +PDEL +AAR +GA F HV++PL PA+ +AI Sbjct: 138 LIIFHVAFQTGFATLFMRNFIAALPDELFQAARAEGATPFQTLIHVVVPLVRPAWAALAI 197 Query: 194 WQFTQIWNEFLFAVTLTRPES-QPITVALAQLAGGEAVKWNLPMAGAILAALPTLLVYIL 252 FT IWN++ +AV LT ++ +P+T LA L G WNL AG I+ A+P ++++ L Sbjct: 198 LLFTFIWNDYFWAVVLTVSDNVKPVTAGLANLRGEWVSAWNLISAGTIIVAVPPVVMFFL 257 Query: 253 LGRYFLRGLLAGSVKG 268 + ++F+ GL G+VKG Sbjct: 258 MQKHFIAGLTMGAVKG 273 Lambda K H 0.330 0.146 0.461 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: 240 Number of extensions: 17 Number of successful extensions: 3 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: 268 Length of database: 273 Length adjustment: 25 Effective length of query: 243 Effective length of database: 248 Effective search space: 60264 Effective search space used: 60264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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