Align required for pyruvate transport, with Pf1N1B4_3673 (actP-like) (characterized)
to candidate GFF2883 Psest_2939 Predicted membrane protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3672 (103 letters) >FitnessBrowser__psRCH2:GFF2883 Length = 104 Score = 136 bits (342), Expect = 8e-38 Identities = 63/102 (61%), Positives = 81/102 (79%) Query: 2 NDSIYLSIQNSPRFKELVSKRERFAWILSAIMLGLYSGFILLIAYGPHILGAKISPESSI 61 N+++Y I +PRF+ELV+KR RFAW+LSA+MLG Y FILLIA+ P ILG +S ++ Sbjct: 3 NENVYRQIYANPRFQELVAKRGRFAWLLSAVMLGAYLAFILLIAFEPQILGVPLSADTVT 62 Query: 62 TWGIPIGVGLIVSAFVLTGIYVRRANGEFDDLNNAILKEAQQ 103 TWGIP+GVG+I AF+LTG+YV+RANGEFD +N IL EAQQ Sbjct: 63 TWGIPVGVGVIFMAFILTGVYVQRANGEFDRINQEILNEAQQ 104 Lambda K H 0.323 0.141 0.413 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: 75 Number of extensions: 2 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: 103 Length of database: 104 Length adjustment: 11 Effective length of query: 92 Effective length of database: 93 Effective search space: 8556 Effective search space used: 8556 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: 40 (21.5 bits) S2: 40 (20.0 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