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 RR42_RS18605 RR42_RS18605 sugar ABC transporter permease
Query= TCDB::Q72KX4 (268 letters) >FitnessBrowser__Cup4G11:RR42_RS18605 Length = 295 Score = 124 bits (310), Expect = 3e-33 Identities = 77/255 (30%), Positives = 131/255 (51%), Gaps = 6/255 (2%) Query: 18 LLPVYLVVLTALKEPARITLETVWQ-WPHPPYWESFRTA-WEAFRPKFQ-NSVVLAVSAT 74 L P Y + +TA K + + + W P + F+ ++ P++ N+V+++ +T Sbjct: 41 LFPFYWMAITAFKPDGELLMRSANPFWVMAPTFAHFKKLLFDTPYPEWLLNTVIVSTIST 100 Query: 75 LLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMKSIGLYGSLFGL 134 S L Y + + F+G+ + + IP + IPL + +GL+ + + L Sbjct: 101 FASLAASVLAAYAIERLRFQGAKQVGLAVFLAYLIPPSILFIPLASIVFQLGLFDTRWAL 160 Query: 135 VLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPLSVPAFVVVAIW 194 +L + + IP T + Y+ IP EL E A IDGA + I +ILPL+VP + I+ Sbjct: 161 ILTYPTFLIPFCTWLLMGYFRSIPYELEECALIDGATRWEILVKIILPLAVPGLISAGIF 220 Query: 195 QFTQIWNEFLFAVT-LTRPESQPITVAL-AQLAGGEAVKWNLPMAGAILAALPTLLVYIL 252 FT WNEF++A+T ++ E + + V + +L G+ W MAGA+L +LP LVY Sbjct: 221 AFTLSWNEFIYALTFISSSEVKTVPVGIVTELIEGDVYHWGALMAGALLGSLPVALVYSF 280 Query: 253 LGRYFLRGLLAGSVK 267 Y++ G + G+VK Sbjct: 281 FVEYYVSG-MTGAVK 294 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: 255 Number of extensions: 15 Number of successful extensions: 2 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: 295 Length adjustment: 26 Effective length of query: 242 Effective length of database: 269 Effective search space: 65098 Effective search space used: 65098 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