Align ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized)
to candidate Pf1N1B4_595 Glucose ABC transport system, inner membrane component 1
Query= reanno::Smeli:SMc04258 (302 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_595 Length = 314 Score = 255 bits (651), Expect = 1e-72 Identities = 129/291 (44%), Positives = 182/291 (62%) Query: 9 ARPNQWLRNLNAKIASIPMILTAMVIFVGGTAWTVVYSFTNSKLLPRLAFVGFDQYERLW 68 A P L+ K+ P +L +V F G WT V SFTNS +P +VG QY RL Sbjct: 22 ASPFDALQRWLPKLVLAPSMLIVLVGFYGYIIWTFVLSFTNSSFMPSYKWVGLQQYIRLM 81 Query: 69 AAPRWLVSIQNLAVFGCLSLVFSLVIGFVLAALMDQKIRFENTFRTIMLYPFALSFIVTG 128 RW V+ +NLAVFG + + SLV+G LA L+DQ+IR E RT+ LYP ALS IVTG Sbjct: 82 DNDRWWVASKNLAVFGGMFIGISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIVTG 141 Query: 129 LVWQWLLNPQYGIQSIVRSLGWTSFSFDPLYNSNIVIYGILIAALWQGTGLVMCLMLAGL 188 W+WLLNP G+ ++R GW F D L + + V+Y ++IAA+WQ +G VM + LAGL Sbjct: 142 TAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFVMAMFLAGL 201 Query: 189 RGIDEDIWKAARVDGIPMWKTYVLIIIPMMRGVFITTLVIIASGIVKVYDLVVAQTSGGP 248 RG+D+ I +AA+VDG + Y+ I++P +R VF + +I+A +K +DLV A T+GGP Sbjct: 202 RGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAGGP 261 Query: 249 GIASEVPAKYVYDYMFQAQNLGQGFAASTMMLVTVAIIIVPWAYLEFGGGR 299 G +S++PA ++Y + F +G G A++ MML + I+VP+ Y E G R Sbjct: 262 GYSSDLPAMFMYSFTFSRGQMGIGSASAMMMLGAILAILVPYLYSELRGKR 312 Lambda K H 0.329 0.142 0.449 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: 360 Number of extensions: 17 Number of successful extensions: 1 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: 302 Length of database: 314 Length adjustment: 27 Effective length of query: 275 Effective length of database: 287 Effective search space: 78925 Effective search space used: 78925 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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