Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate GFF4517 PS417_23120 aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__WCS417:GFF4517 Length = 382 Score = 179 bits (453), Expect = 2e-49 Identities = 122/358 (34%), Positives = 186/358 (51%), Gaps = 11/358 (3%) Query: 35 LLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAVDAE- 93 L LS G PDF P ++ A + G+ YA + G LRQ++A + R G VDA+ Sbjct: 27 LNLSQGFPDFSGPQGLLDAVGKHIALGHNQYAPMTGLPVLRQQVAAKIARSYGATVDADS 86 Query: 94 QVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENGFRV 153 +V + GA A++ +Q ++ GDEVIV +P Y +YE G R V V + S +GF + Sbjct: 87 EVTITPGATEAIFCAIQAVIRNGDEVIVFDPSYDSYEPSVELAGGRCVHVQL-SLSGFAL 145 Query: 154 QAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELLFD 213 E++ A ++PRTR + LN+PHNP+GA + RA + LAEL D++++SDEVY L+FD Sbjct: 146 DFEKIKAALSPRTRMIILNTPHNPTGALISRAELDQLAELIRDRDIYLVSDEVYEHLVFD 205 Query: 214 G-EHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGSPE 272 G HVS + + R ++S K++ +TGW+ G+VV P AL A L + + + Sbjct: 206 GVAHVSVLAHEELYPRAFVVSSFGKTYHVTGWKTGYVVAPPALTAELRKVHQYVNFCGVT 265 Query: 273 FIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVD---IR 329 +Q A + +E + Y+ +RDL + LA S R G F +VD IR Sbjct: 266 PLQYALADFMAEHPEHVEELPAFYQAKRDLFCDLLAAS-RFSFTRVTGTYFQLVDYSQIR 324 Query: 330 PTGLSAQAFADRLLDRHGVSVLAGEAF---GPSAAGHIRLGLVLGAEPLREACRRIAL 384 P L A + + HGV+ + F P +RL E LR+A ++ + Sbjct: 325 P-DLDDVAMSLWMTREHGVATIPVSVFYQTPPQGQRLVRLCFAKREETLRQAAEKLCV 381 Lambda K H 0.322 0.136 0.411 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: 386 Number of extensions: 22 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: 393 Length of database: 382 Length adjustment: 30 Effective length of query: 363 Effective length of database: 352 Effective search space: 127776 Effective search space used: 127776 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: 50 (23.9 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