Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate SMc03063 SMc03063 alpha-glucoside ABC transporter permease
Query= uniprot:A8LLL4 (385 letters) >FitnessBrowser__Smeli:SMc03063 Length = 380 Score = 447 bits (1149), Expect = e-130 Identities = 227/383 (59%), Positives = 289/383 (75%), Gaps = 15/383 (3%) Query: 8 KSSLTWAVQLSVVGLVVLWLLPTFGLFVSSFRTVEQISSSGWWKAMFPSEQNLTLRAADP 67 +S LTWAV LSV+ LV+LW LPT GL +SS R +Q++ SGWW A+ S +N +RA Sbjct: 6 RSPLTWAVHLSVLLLVLLWTLPTAGLLISSLRDKDQLAVSGWWTALSSSSRNAVVRAPSA 65 Query: 68 DDFRMPQGDLFVVKGNLFEDEGISEAEISVWGTSSRDVAAYTAGETADLGDGETITVQSN 127 +D ++ + FV+ GNL E G E+S +G SSR+ + GETA+L DGE +TVQS+ Sbjct: 66 ED-QVERDGKFVISGNLLEGRG----EVSAFGFSSREPTKFKPGETAELNDGERLTVQSD 120 Query: 128 GAYVWSGTDDQISGRGQRVFVTATTPPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIP 187 G++ RGQR+F TATTPP FT NY +L ++ G+ R+F N+LTV +P Sbjct: 121 GSFEIVSDQRMEGSRGQRIFFTATTPPRFTLDNYAEVL----SAAGIGRSFLNSLTVAVP 176 Query: 188 ATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLHNAIGI----- 242 +T+IPIL+AAFAAYALAWM FPGRA+L+A++VGLLVVPLQ++LIPLL L+N +G Sbjct: 177 STVIPILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVS 236 Query: 243 GKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLPLSFPA 302 K Y+G WLAHTGFG+PLAIYLLRNYM GLPR+I+E+A+VDGA+DF IF KI+LPLSFPA Sbjct: 237 AKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFDIFVKIILPLSFPA 296 Query: 303 LASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEILATAAFVSIA 362 LASFAIFQFLWTWNDLLVA VFL A V+T ++V LLG+RGGNWEIL +AF++I Sbjct: 297 LASFAIFQFLWTWNDLLVAIVFL-GAGDDKLVLTGRLVNLLGSRGGNWEILTASAFITIV 355 Query: 363 VPLLVFFSMQRFLVRGLLAGSVK 385 VPL+VFF++QR+LVRGLLAGSVK Sbjct: 356 VPLIVFFALQRYLVRGLLAGSVK 378 Lambda K H 0.323 0.138 0.419 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: 450 Number of extensions: 17 Number of successful extensions: 5 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: 385 Length of database: 380 Length adjustment: 30 Effective length of query: 355 Effective length of database: 350 Effective search space: 124250 Effective search space used: 124250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 50 (23.9 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