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 BPHYT_RS29180 BPHYT_RS29180 sugar ABC transporter permease
Query= TCDB::Q72KX4 (268 letters) >FitnessBrowser__BFirm:BPHYT_RS29180 Length = 306 Score = 215 bits (547), Expect = 1e-60 Identities = 113/275 (41%), Positives = 175/275 (63%), Gaps = 13/275 (4%) Query: 6 LYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEA------- 58 +Y FLL A FFLLP+Y++++T++K I L + +P ++ AW++ Sbjct: 33 VYAFLLTAALFFLLPLYVMLVTSVKPMNEIRLGNLLAFPTHFTLSAWSAAWQSACTGLDC 92 Query: 59 --FRPKFQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILI 116 + F NSV + V +T+LS +G++NGY L+ W RG+GLLF ++L G FIP Q ++ Sbjct: 93 NGIQVGFWNSVRIVVPSTILSIAIGAVNGYALSFWRPRGAGLLFGVLLMGAFIPVQVMVY 152 Query: 117 PLFQFMKSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIF 176 PL + + S+ L+ SL G+V++H I+G+P++TL+FRNYY IP EL +AARIDG GF+ IF Sbjct: 153 PLVRVLASVHLFSSLPGIVVIHTIFGMPVMTLLFRNYYVSIPQELFKAARIDGGGFWRIF 212 Query: 177 RHVILPLSVPAFVVVAIWQFTQIWNEFLFAVTLTRPESQPITVALAQLAG---GEAVKWN 233 ++LP+S P VV I Q T IWN+F+ + ++ P+TV L + GE + +N Sbjct: 213 VQLMLPMSTPIIVVAVIMQVTGIWNDFILGLVFAGTKNLPMTVQLNNIINTTTGERL-YN 271 Query: 234 LPMAGAILAALPTLLVYILLGRYFLRGLLAGSVKG 268 + MA IL ++ L VY + GR+F+RG+ +G+VKG Sbjct: 272 VNMAATILTSMVPLAVYFVSGRWFVRGIASGAVKG 306 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: 286 Number of extensions: 13 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: 306 Length adjustment: 26 Effective length of query: 242 Effective length of database: 280 Effective search space: 67760 Effective search space used: 67760 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