Align Aspartate/glutamate permease AcaP (characterized)
to candidate 15023 b0899 putative transport (VIMSS)
Query= SwissProt::A2RL65 (489 letters) >FitnessBrowser__Keio:15023 Length = 476 Score = 582 bits (1500), Expect = e-170 Identities = 278/473 (58%), Positives = 363/473 (76%), Gaps = 4/473 (0%) Query: 4 KKIRWFTVAFIAFNMVWGMGNVVNNFAQQGITVVTSWLLILALYFIPYALIVGQLCSTFK 63 K++RW+ +A ++F VWG GNVVNN+A QG+ VV SW+ I ALYF PYALIVGQL STFK Sbjct: 8 KQLRWYNIALMSFITVWGFGNVVNNYANQGLVVVFSWVFIFALYFTPYALIVGQLGSTFK 67 Query: 64 DSKGGVSSWVENTSTKRLAYYAAWTYWVVHIPYLAQKPQAILIAFGWVGQGNGNLVSQMS 123 D KGGVS+W+++T LAY AAWTYWVVHIPYLAQKPQAILIA GW +G+G+L+ + S Sbjct: 68 DGKGGVSTWIKHTMGPGLAYLAAWTYWVVHIPYLAQKPQAILIALGWAMKGDGSLIKEYS 127 Query: 124 MTAVALISLAIFLAFLWLSTKGLNTLKVIGGLAGTAMFVMSLLFIVMAIGAPFIAKDFHI 183 + A+ ++L +F+ F+W++++G+ +LK++G +AG AMFVMSLL++ MA+ AP I + HI Sbjct: 128 VVALQGLTLVLFIFFMWVASRGMKSLKIVGSVAGIAMFVMSLLYVAMAVTAPAIT-EVHI 186 Query: 184 ATPDMGNIKTYIPKFDFSYFTTISMLVFAVGGAEKISPYVNQTKNPAKEFPRGMFLLAGM 243 AT ++ +T+IP DF+Y TTISMLVFAVGGAEKISPYVNQT+NP KEFP+GM LA M Sbjct: 187 ATTNI-TWETFIPHIDFTYITTISMLVFAVGGAEKISPYVNQTRNPGKEFPKGMLCLAVM 245 Query: 244 VGICAVLGSIAMGMIFSSGNLPKDLMANGAYAAFQILGQHFGVGNFLMIVYALTNGVGQI 303 V +CA+LGS+AMGM+F S N+P DLM NG Y AFQ LG+++ +GN LM++YA+ N +GQ+ Sbjct: 246 VAVCAILGSLAMGMMFDSRNIPDDLMTNGQYYAFQKLGEYYNMGNTLMVIYAIANTLGQV 305 Query: 304 AALAFSIDAPLRILLADADPEYVPAWLRKKTNKGTLKNGYTLTGILVSIIILLPLLGIGD 363 AAL FSIDAPL++LL DAD +Y+PA L + GT NGY LT +LV+I+I+LP LGIGD Sbjct: 306 AALVFSIDAPLKVLLGDADSKYIPASLCRTNASGTPVNGYFLTLVLVAILIMLPTLGIGD 365 Query: 364 MNELVKWLTNLNSVVMPMRYLWVFFAFIMLNRAVKHFQSEYKFIKQKRLAMIAGAWCFLF 423 MN L KWL NLNSVVMP+RYLWVF AFI + R + ++ EY FI+ K LAM G WCF F Sbjct: 366 MNNLYKWLLNLNSVVMPLRYLWVFVAFIAVVRLAQKYKPEYVFIRNKPLAMTVGIWCFAF 425 Query: 424 TLIACVLGMVPKLDYAANPSAWWFQLASNILTPIVLILLGMLLPFIARREQRK 476 T AC+ G+ PK++ A + W FQLA N+ TP VL+ LG++ P +AR+ K Sbjct: 426 TAFACLTGIFPKME--AFTAEWTFQLALNVATPFVLVGLGLIFPLLARKANSK 476 Lambda K H 0.328 0.140 0.438 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: 774 Number of extensions: 23 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: 489 Length of database: 476 Length adjustment: 34 Effective length of query: 455 Effective length of database: 442 Effective search space: 201110 Effective search space used: 201110 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 52 (24.6 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