Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate WP_019868505.1 METMI_RS0122225 sulfate ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >NCBI__GCF_000384075.1:WP_019868505.1 Length = 347 Score = 192 bits (487), Expect = 2e-53 Identities = 104/250 (41%), Positives = 149/250 (59%), Gaps = 11/250 (4%) Query: 20 AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDI 79 A++ +D+ I +GE + L+GPSGCGK+T LR++AGLE + G + + D T R I Sbjct: 17 ALNNIDLEIPEGELVALLGPSGCGKTTLLRIIAGLEQADSGRVVLNGEDKTEQHVSHRGI 76 Query: 80 AMVFQNYALYPHMTVADNMGFALKIAGVPK------AEIRQKVEEAAKILDLTQYLDRKP 133 VFQ+YAL+ HMTV DN+ F L++ PK A+I +KV +++ L DR P Sbjct: 77 GFVFQHYALFRHMTVFDNIAFGLRVK--PKKHRPSEADIAKKVHALLELVQLDWLHDRFP 134 Query: 134 KALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVT 193 LSGGQRQR+A+ RA+ EP V L+DEP LDA +R R + +L L +T+++VT Sbjct: 135 DQLSGGQRQRIALARALAVEPDVLLLDEPFGALDASVRKDLRQWLRNLHHELNVTSIFVT 194 Query: 194 HDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGV 253 HDQ EAM + +V VL G ++Q +P ++YD PAN FV+ FIG + P + Sbjct: 195 HDQEEAMEVASQVVVLNHGRIEQQGAPSDIYDHPANAFVSRFIG---QTNIFAPDDHDAI 251 Query: 254 KFGNSVVPVN 263 S +PVN Sbjct: 252 WLQTSGLPVN 261 Lambda K H 0.317 0.135 0.379 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: 279 Number of extensions: 13 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: 377 Length of database: 347 Length adjustment: 29 Effective length of query: 348 Effective length of database: 318 Effective search space: 110664 Effective search space used: 110664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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