Align Aspartate/glutamate permease AcaP (characterized)
to candidate WP_022529769.1 L248_RS08515 amino acid permease
Query= SwissProt::A2RL65 (489 letters) >NCBI__GCF_000469325.1:WP_022529769.1 Length = 480 Score = 590 bits (1522), Expect = e-173 Identities = 274/473 (57%), Positives = 358/473 (75%), Gaps = 1/473 (0%) Query: 2 DTKKIRWFTVAFIAFNMVWGMGNVVNNFAQQGITVVTSWLLILALYFIPYALIVGQLCST 61 + K++RW+ +A +AF VWG+GNVVNNF QG+TVV SW+LI+ LYF+PY L+VGQL +T Sbjct: 4 EQKQLRWYNIALLAFVAVWGLGNVVNNFYNQGLTVVVSWILIMILYFVPYTLMVGQLGAT 63 Query: 62 FKDSKGGVSSWVENTSTKRLAYYAAWTYWVVHIPYLAQKPQAILIAFGWVGQGNGNLVSQ 121 F GGVSSW++N S KRLAY+AAWTYWVVH+PYLAQKPQAI+IAF W+ Q NG +++ Sbjct: 64 FATEGGGVSSWIQNLSGKRLAYFAAWTYWVVHVPYLAQKPQAIMIAFSWLFQSNGKFINE 123 Query: 122 MSMTAVALISLAIFLAFLWLSTKGLNTLKVIGGLAGTAMFVMSLLFIVMAIGAPFIAKDF 181 + V + L +FL F+W+S++G+ TL +G +AG+AMFV+S+LFI++ + AP + Sbjct: 124 SNPLIVQTLCLVLFLLFMWMSSRGITTLNRLGSIAGSAMFVLSILFIILGVSAPMMTGS- 182 Query: 182 HIATPDMGNIKTYIPKFDFSYFTTISMLVFAVGGAEKISPYVNQTKNPAKEFPRGMFLLA 241 IAT M + +YIPKFDF+Y TTI+MLVFAVGGAEKISPYVN+T NPAKEFP+GM LA Sbjct: 183 SIATAHMDQLSSYIPKFDFNYLTTIAMLVFAVGGAEKISPYVNKTHNPAKEFPKGMIALA 242 Query: 242 GMVGICAVLGSIAMGMIFSSGNLPKDLMANGAYAAFQILGQHFGVGNFLMIVYALTNGVG 301 MV + A+LGS AMGMIF + ++P DL ANGAY AFQ LG + VGN M +YA+TN + Sbjct: 243 IMVAVSAILGSFAMGMIFDAHHMPADLYANGAYMAFQRLGDFYHVGNIFMWIYAVTNAMA 302 Query: 302 QIAALAFSIDAPLRILLADADPEYVPAWLRKKTNKGTLKNGYTLTGILVSIIILLPLLGI 361 +AALA SIDAPLR+LLADAD ++P + K ++G NGY +T +LV +II++P LGI Sbjct: 303 SMAALAVSIDAPLRMLLADADTHFIPKAMTKTNSRGVYINGYKMTAVLVGLIIMIPALGI 362 Query: 362 GDMNELVKWLTNLNSVVMPMRYLWVFFAFIMLNRAVKHFQSEYKFIKQKRLAMIAGAWCF 421 MN L WL NLN++VMPMRYLWVF A+++L+R + F S+Y F+K K +A I G WCF Sbjct: 363 HGMNGLYGWLLNLNAIVMPMRYLWVFLAYMLLSRQMDKFHSDYMFVKNKSVAFIFGLWCF 422 Query: 422 LFTLIACVLGMVPKLDYAANPSAWWFQLASNILTPIVLILLGMLLPFIARREQ 474 LFT AC+LGM PK +A + WWFQLA N+LTPIVL+LLG++LP IARR + Sbjct: 423 LFTAFACILGMTPKAAFAGDTKTWWFQLALNVLTPIVLLLLGLILPIIARRHE 475 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: 795 Number of extensions: 31 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: 489 Length of database: 480 Length adjustment: 34 Effective length of query: 455 Effective length of database: 446 Effective search space: 202930 Effective search space used: 202930 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 24 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