Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate 3608192 Dshi_1597 ABC transporter related (RefSeq)
Query= uniprot:Q88GX0 (260 letters) >FitnessBrowser__Dino:3608192 Length = 355 Score = 152 bits (383), Expect = 1e-41 Identities = 88/240 (36%), Positives = 137/240 (57%), Gaps = 11/240 (4%) Query: 20 LIRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQV 79 LIRI+ + K+YG++H LRD+ + + GE L GPSG GK+TL+R I E + G++ + Sbjct: 5 LIRIQNVQKYYGSYHALRDVSVDIGAGEFFSLLGPSGCGKTTLLRTIAGFEEFESGTLTL 64 Query: 80 DGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNC---LLAPTSVRGLSRKDAEERA 136 G+D+ + MVFQ + +FPH+SV DN L T + G +R A Sbjct: 65 GGVDMVGVPAN----KRPTNMVFQSYAIFPHLSVGDNVGFGLRRRTDLTGEARASLVADA 120 Query: 137 RMYLSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLD 196 L VG++ + LSGGQ+QRVA+ARAL +KP+++L DEP SALD +M ++ Sbjct: 121 ---LHMVGLKGYGARAAHALSGGQRQRVALARALVLKPKVLLLDEPLSALDKKMREQMQT 177 Query: 197 VLVQL-AGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERAKAFL 255 L +L G+T + VTH+ A +++R+ + G+I + +PPQ + QP + F+ Sbjct: 178 ELRRLQRHVGITFILVTHDQEEALTMSDRIAVMFEGRIAQLAPPQTLYAQPASRAVAEFI 237 Lambda K H 0.322 0.137 0.395 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: 215 Number of extensions: 11 Number of successful extensions: 4 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: 260 Length of database: 355 Length adjustment: 27 Effective length of query: 233 Effective length of database: 328 Effective search space: 76424 Effective search space used: 76424 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: 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