Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 191 bits (484), Expect = 3e-53 Identities = 111/324 (34%), Positives = 181/324 (55%), Gaps = 33/324 (10%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 M+ + + + VL+G++L + GE L+GPSGCGK+TLLRT+AGL+ +G+I Sbjct: 1 MSTLSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSI 60 Query: 61 SIDGKKIND----IEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNE 116 +I+GK ++ + P+ R I M+FQ YAL+PH+TVA+N+ FG++ + + + R+ E Sbjct: 61 AINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGVRQLDKQSRSV--RLEE 118 Query: 117 ISELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEI 176 + L++++ L R P ELSGGQ+QRV++ RAL+ + ++L DEP SN+DA +R + LEI Sbjct: 119 MLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEI 178 Query: 177 KRLHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGS 236 + + + ++VTH + EA D +A+ + G I Q G P +Y P ++A F+G+ Sbjct: 179 RAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLGA 238 Query: 237 PEMNFLEG--------AVLEKIPWPEARKADQILG---IRPDAFALNQGPLGTQE----- 280 N+L+ + L P P+ KA G +RP+ + G E Sbjct: 239 --SNYLDVRLEAGQLISTLGAFPLPQDFKAASETGRWLLRPEQLLIEARADGAGEILERR 296 Query: 281 ---------VALGDFQIDISENLG 295 V LG+ +DI +LG Sbjct: 297 FLGNGCHYLVRLGEQVLDIHSHLG 320 Lambda K H 0.318 0.136 0.383 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: 8 Number of successful extensions: 3 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: 347 Length of database: 341 Length adjustment: 29 Effective length of query: 318 Effective length of database: 312 Effective search space: 99216 Effective search space used: 99216 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 (21.7 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