Align Trehalose permease IIC protein (characterized, see rationale)
to candidate Pf1N1B4_836 PTS system, trehalose-specific IIB component (EC 2.7.1.69) / PTS system, trehalose-specific IIC component (EC 2.7.1.69)
Query= uniprot:A0A0N9WDQ5 (480 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_836 Length = 480 Score = 882 bits (2279), Expect = 0.0 Identities = 448/480 (93%), Positives = 463/480 (96%) Query: 1 MSHDYPTIASELLHSLGGADNLEQAAHCVTRLRLALKDPQRVDSATLNQIDLVKGSFFTG 60 MSHDYP I +ELLHSLGG+DNLEQAAHCVTRLRLALKDP VDSATLNQIDLVKGSF+TG Sbjct: 1 MSHDYPNIVTELLHSLGGSDNLEQAAHCVTRLRLALKDPSLVDSATLNQIDLVKGSFYTG 60 Query: 61 GLFQVVIGPGEVEKVYAALRQQTGLAASTIADVKQKGADKTNAMQRLVRVFSDVFMPILP 120 GLFQVVIGPGEVEKVYA LR+QTGLA STIADVKQK ADK + MQRLVRVFSDVFMPILP Sbjct: 61 GLFQVVIGPGEVEKVYAELRRQTGLAVSTIADVKQKSADKIHPMQRLVRVFSDVFMPILP 120 Query: 121 ALIIAGLLMGVNNLIGAKGMFIAGKTLLEAYPTLDGVWSLINLMANTSFVFLPALVGWSA 180 ALIIAGLLMG+NNLIGAKGMFI GKTLL+AYP LDG+WSLINLMANTSFVFLPALVGWSA Sbjct: 121 ALIIAGLLMGINNLIGAKGMFIEGKTLLDAYPKLDGLWSLINLMANTSFVFLPALVGWSA 180 Query: 181 AKRFGGSEILGIVLGLMLVHPDLLNAWNYGKAVAGLDGQSLPYFDIFGWFKIEKVGYQGQ 240 AKRFGGSEILGIVLGLMLVHPDLLNAWNYGKAVAGL+GQSLPYFDI G F+IEKVGYQGQ Sbjct: 181 AKRFGGSEILGIVLGLMLVHPDLLNAWNYGKAVAGLEGQSLPYFDILGMFQIEKVGYQGQ 240 Query: 241 ILPILMAAYVMSVIEKWLRARVPNAIQLLVVPITTIVVTGVLALAVIGPVTRHLGILITE 300 ILPILMAAYVMSVIEKWLRARVPNA+QLLVVPITTIVVTGVLALAVIGPVTRHLGILITE Sbjct: 241 ILPILMAAYVMSVIEKWLRARVPNAVQLLVVPITTIVVTGVLALAVIGPVTRHLGILITE 300 Query: 301 GVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQ 360 GVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQ Sbjct: 301 GVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQ 360 Query: 361 GSAALGVFYMTRSARDKSMASTSAISAYFGITEPAMFGVNLRYKFPFYAALSGSALGCMF 420 GSAAL VFYMTRS RDKSMASTSAISAYFGITEPAMFGVNLRYKFPFYAAL GSALGC+F Sbjct: 361 GSAALAVFYMTRSVRDKSMASTSAISAYFGITEPAMFGVNLRYKFPFYAALIGSALGCIF 420 Query: 421 LSLNKVQASAIGVGGLPGFISIIPQFIPMFIVGMVIAMVVPFVLTCGMSMKIVRAGYRVA 480 LSLNKVQASAIGVGGLPGFISIIPQFIPMF+VGMVIAMVVPFVLTCG+SM+IVR GYRVA Sbjct: 421 LSLNKVQASAIGVGGLPGFISIIPQFIPMFVVGMVIAMVVPFVLTCGLSMRIVRPGYRVA 480 Lambda K H 0.326 0.141 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: 905 Number of extensions: 27 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: 480 Length of database: 480 Length adjustment: 34 Effective length of query: 446 Effective length of database: 446 Effective search space: 198916 Effective search space used: 198916 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 (21.7 bits) S2: 51 (24.3 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