Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 197 bits (501), Expect = 4e-55 Identities = 113/299 (37%), Positives = 178/299 (59%), Gaps = 16/299 (5%) Query: 1 MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60 M++++++ + Y G + R ++L + GE +GPSGCGK+TLLR IAGL+DI++G + Sbjct: 1 MSTLSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSI 60 Query: 61 LIDNQRVND----LPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEA 116 I+ + V+ + P+ RS+GM+FQ YAL+PH+TVA+N+ FG++ +DK+ R+E Sbjct: 61 AINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGVR--QLDKQSRSVRLEE 118 Query: 117 VAEILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEI 176 + +++L+ L +R P +LSGGQ+QRV+I R + EP + L DEP SN+DA +R + +EI Sbjct: 119 MLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEI 178 Query: 177 ARLHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGS 236 + + + ++VTH + EA AD + + AG I Q G P LY P +VA FLG+ Sbjct: 179 RAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLGA 238 Query: 237 PQMNFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEAD 295 N+++VR + I +P LP D A S L RPE ++ AD Sbjct: 239 --SNYLDVRLEAGQ----LISTLGAFP--LPQDFKAASETGRWLL--RPEQLLIEARAD 287 Lambda K H 0.322 0.139 0.405 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: 303 Number of extensions: 13 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: 371 Length of database: 341 Length adjustment: 29 Effective length of query: 342 Effective length of database: 312 Effective search space: 106704 Effective search space used: 106704 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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