Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate GFF3990 Psest_4063 sulfate ABC transporter, ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__psRCH2:GFF3990 Length = 334 Score = 109 bits (273), Expect = 6e-29 Identities = 78/228 (34%), Positives = 121/228 (53%), Gaps = 7/228 (3%) Query: 1 MTLRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGT-V 59 M++ ++ +G + LN ++L + +G++ AL+GP+GCGK++LL + L P SG+ V Sbjct: 1 MSIEISHINKRFGQFQALNTINLHIQSGELVALLGPSGCGKTSLLRIIAGLETPDSGSIV 60 Query: 60 FLGDNPINMLSSRQLA-RRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNAR 118 F G++ +SSR + R + + QH+ +TV E V++G A + Sbjct: 61 FHGED----VSSRDVRDRNVGFVFQHYALFRHMTVFENVAFGLRMKPKKQRPSEAVIAEK 116 Query: 119 VNVAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLM 178 V+ + +++ LA R +LSGGQRQR LA LA V+LLDEP LD + +L Sbjct: 117 VHELLGLVQLDWLADRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELR 176 Query: 179 RLMGELRTQ-GKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEV 225 R + L T V V HD +A D++VVM G + GTP EV Sbjct: 177 RWLARLHEDVHLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGTPAEV 224 Lambda K H 0.320 0.134 0.393 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: 171 Number of extensions: 12 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: 255 Length of database: 334 Length adjustment: 26 Effective length of query: 229 Effective length of database: 308 Effective search space: 70532 Effective search space used: 70532 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 (21.8 bits) S2: 48 (23.1 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