Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)
Query= TCDB::O05177 (398 letters) >FitnessBrowser__ANA3:7024902 Length = 320 Score = 105 bits (261), Expect = 2e-27 Identities = 105/356 (29%), Positives = 161/356 (45%), Gaps = 78/356 (21%) Query: 33 LVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIVAFVG 92 LV F F +G ++ TNL+ N+F++I ALGM LVI++G IDLSVG+++A G Sbjct: 21 LVGTFQFDGFASGRVV------TNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSG 74 Query: 93 AIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFRGLTLF 152 + ++L ++ +P LA ++ L +G + GA G I +++ FIVTLAGM + RGL Sbjct: 75 VVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLAT- 133 Query: 153 VLGGKNIG---PFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRVVN 209 L ++I PF +S LP G ++ + ++ V+I V + Y Sbjct: 134 TLSEESIAIDHPFYDAVAEMSIA-LPGNGALDLSSLIFILFFVIIAVVMHY--------- 183 Query: 210 VKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRTTI 269 + G +V G G Q S L +TTI Sbjct: 184 TRFGTNVYAIG----------------GNQHSA---------------ELMGISIAKTTI 212 Query: 270 GRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGFEL 329 +YA+ + L+GI +F TF G G G+ EL Sbjct: 213 S--IYAI--SSFLATLAGI---VFTFYTF--SGYALGAIGV-----------------EL 246 Query: 330 DVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVG-LGIDFQQMVKGLVL 384 D IAA IGG +GG G + G V+G +MGV+ ++ G L + ++V GL+L Sbjct: 247 DAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLL 302 Score = 25.8 bits (55), Expect = 0.002 Identities = 47/222 (21%), Positives = 90/222 (40%), Gaps = 37/222 (16%) Query: 28 GMLIALVAIMVFFQFYTGGILFRPVNLT----NLILQNSFIVIMALGMLLVIVAGHIDLS 83 G +I + + F G L R + T ++ + + F +A + + G +DLS Sbjct: 107 GTIIHVYKLQPFIVTLAGMFLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLS 166 Query: 84 VGSIVAFVGAIAAILT-VQWGMNPFLAALICLVIGGIIGAAQ-------GYWIAYHRIPS 135 + F IA ++ ++G N + IGG +A+ I+ + I S Sbjct: 167 SLIFILFFVIIAVVMHYTRFGTNVY-------AIGGNQHSAELMGISIAKTTISIYAISS 219 Query: 136 FIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPD--IGGIEGLNTTSMILTVL 193 F+ TLAG++ T + G +G + I+ + + G G +++ +L Sbjct: 220 FLATLAGIV----FTFYTFSGYALGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVIL 275 Query: 194 ITVALFYL-------AWRRRVVNVKHGIDVEPFGFFIVQNLL 228 + V Y+ +W ++V I + F F ++Q LL Sbjct: 276 MGVIQTYITFDGSLSSWWTKIV-----IGLLLFFFILLQKLL 312 Lambda K H 0.329 0.145 0.422 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: 437 Number of extensions: 26 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 398 Length of database: 320 Length adjustment: 29 Effective length of query: 369 Effective length of database: 291 Effective search space: 107379 Effective search space used: 107379 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: 49 (23.5 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