Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate Pf1N1B4_594 Glucose ABC transport system, inner membrane component 2
Query= uniprot:A8LLL4 (385 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_594 Length = 281 Score = 115 bits (289), Expect = 1e-30 Identities = 66/208 (31%), Positives = 102/208 (49%), Gaps = 1/208 (0%) Query: 178 FFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLH 237 F+N++ +T+PA +I + A Y L+ F G L L++ +P Q L+P Sbjct: 74 FWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTL 133 Query: 238 NAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLP 297 IG+ G L H +G+ RNY V +P +++ A++DGA F IF KI+LP Sbjct: 134 GKIGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFWKILLP 193 Query: 298 LSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEILATAA 357 +S P + I+QF WND L VF TV N +V T + + AA Sbjct: 194 MSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVN-TSTGAKEYNVDMAAA 252 Query: 358 FVSIAVPLLVFFSMQRFLVRGLLAGSVK 385 ++ LLV+ ++ +RGL +G+VK Sbjct: 253 MIAGLPTLLVYIFAGKYFLRGLTSGAVK 280 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: 280 Number of extensions: 18 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: 385 Length of database: 281 Length adjustment: 28 Effective length of query: 357 Effective length of database: 253 Effective search space: 90321 Effective search space used: 90321 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: 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