Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate Pf1N1B4_3771 Transcriptional regulator, GntR family domain / Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::A0A060PQX5 (417 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3771 Length = 388 Score = 254 bits (650), Expect = 2e-72 Identities = 142/393 (36%), Positives = 223/393 (56%), Gaps = 15/393 (3%) Query: 22 FSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQ 81 FS++ +K+S +RE+L + +V+S AGGLPA P A++ + Q Sbjct: 3 FSERVSRLKSSLIREILAAAQRPEVMSFAGGLPAEAMLPKVEWADMPLSMG--------Q 54 Query: 82 YGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAP 141 YG ++G LR ALA R +P +++ SGSQQ LDL +++I+ G +++EAP Sbjct: 55 YGMSEGEPALREALAAEARA-LGVPCEASQVLVVSGSQQTLDLAAKLYIDKGTEILLEAP 113 Query: 142 TYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGV 201 TYLAALQ F+ + + + +PL+ +G + L +L++ K +Y IPTFQNP+ V Sbjct: 114 TYLAALQIFQLFGADCITVPLEADGPNLAQLRNRLEK-----HKPAFIYLIPTFQNPSAV 168 Query: 202 TMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILA 261 SE +R + L E+ ++ED PY EL + G PI + ++ +Y GT SK L Sbjct: 169 RYSEAKRDAVAALLDEFGVTLIEDEPYRELTFDGGSATPIVSRLNKASWIYTGTVSKTLL 228 Query: 262 PGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPR 321 PG R+G++ A P L L KQS DL TN Q A +++ H+ + +FY+ R Sbjct: 229 PGLRVGYLIASPDLFAHLLRLKQSADLHTNRIGQWQALQWIGTEKYQQHLGELRDFYRVR 288 Query: 322 RDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAH 381 RDA ALE + +W P+GG+F W+TL + +DT+ +L+ A+A VA++PGE FF Sbjct: 289 RDAFQSALETHFSDLAQWNVPQGGLFFWLTLKQPLDTRTLLKAALAADVAFMPGEPFFPE 348 Query: 382 RDVK-NTMRLNFTYVPEEKIREGIKRLAETIKE 413 D +RLNF+++ ++ EG+KRLA +++ Sbjct: 349 PDNNPGHLRLNFSHIDPARLDEGLKRLATVVRQ 381 Lambda K H 0.318 0.137 0.398 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: 422 Number of extensions: 22 Number of successful extensions: 5 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: 417 Length of database: 388 Length adjustment: 31 Effective length of query: 386 Effective length of database: 357 Effective search space: 137802 Effective search space used: 137802 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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