Align ATPase (characterized, see rationale)
to candidate GFF3101 Psest_3160 ABC-type polar amino acid transport system, ATPase component
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__psRCH2:GFF3101 Length = 255 Score = 302 bits (773), Expect = 5e-87 Identities = 159/247 (64%), Positives = 188/247 (76%), Gaps = 3/247 (1%) Query: 15 ASAPETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESH 74 AS P +I +GV KW+G QF L ++L+V++GE +V+ GPSGSGKST +R LN LE H Sbjct: 11 ASGP--VIQMQGVHKWFG-QFHVLKDINLSVRQGERIVLCGPSGSGKSTTIRCLNRLEEH 67 Query: 75 QRGEIWIEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQA 134 Q+G I I G L+ D + I IR EVGMVFQ FNLFPHLTVLQN LAP+ VR+ P QA Sbjct: 68 QQGRIVINGVELTSDLKQIEAIRSEVGMVFQHFNLFPHLTVLQNCTLAPMWVRKLPRRQA 127 Query: 135 EATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVR 194 E A LERVRI EQA+K+PGQLSGGQQQRVAIARAL M+P+I+LFDEPTSALDPEMV+ Sbjct: 128 EEIAMHYLERVRIPEQANKFPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVK 187 Query: 195 EVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAK 254 EVLD M LA GMTML THE+GFAR VADRV+ M G+IVE+A P+ FFT P +DR K Sbjct: 188 EVLDTMVSLAESGMTMLCVTHEMGFARTVADRVIFMDKGEIVEQAEPEMFFTNPVNDRTK 247 Query: 255 QFLAQIL 261 FL+QIL Sbjct: 248 LFLSQIL 254 Lambda K H 0.321 0.134 0.387 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: 226 Number of extensions: 5 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 261 Length of database: 255 Length adjustment: 24 Effective length of query: 237 Effective length of database: 231 Effective search space: 54747 Effective search space used: 54747 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: 47 (22.7 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