Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate NP_661016.1 CT0110 class I aminotransferase
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000006985.1:NP_661016.1 Length = 397 Score = 289 bits (739), Expect = 1e-82 Identities = 147/396 (37%), Positives = 237/396 (59%), Gaps = 9/396 (2%) Query: 22 FSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQ 81 FSK +++S +REL+ L D++S AGG+P E FP++ + E+ + + K A Q Sbjct: 4 FSKSVSALRSSAIRELMSLASRPDILSFAGGMPGNELFPIDEVEELFRNLDTKTKQAAFQ 63 Query: 82 YGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAP 141 YG T G L +L ++ ++ +P+ K +MIT+GSQQAL + R F++PGD V+ E P Sbjct: 64 YGPTPGLPSLLESLGGFLERK-GLPVKKNRLMITTGSQQALSIFARAFVDPGDRVLTEYP 122 Query: 142 TYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGV 201 ++ A+ AF+ E V +P+D+ G+ + +L ++++ + K +Y P F NPAG+ Sbjct: 123 CFIGAIAAFRACGAEIVSLPVDEAGIDIAMLRQEVENPDP----AKFLYITPYFHNPAGM 178 Query: 202 TMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGE---PVKPIKAWDDEG-RVMYLGTFS 257 S R+++L++ D ++ED+ YG+L +S E ++PIKA D E V Y+G+FS Sbjct: 179 LYSTNRKRKLIKALQGRDIPLLEDDAYGDLWFSDEHREALQPIKAIDPEDIDVCYMGSFS 238 Query: 258 KILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEF 317 KIL PG R+GW+ A + K E+ KQS D C++ F+QVIA ++ G +D ++ ++ E Sbjct: 239 KILGPGLRLGWMLAPEAIYEKCELIKQSADACSSSFTQVIADAFIRSGRIDTYVASVREE 298 Query: 318 YKPRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEA 377 YK R +M+KAL +P VRW +P+GG ++W+TLPEG D +L++A+ G +V G Sbjct: 299 YKRRAASMVKALRSNLPAYVRWNEPKGGFYIWLTLPEGADATEILKRAIEGGAVFVTGST 358 Query: 378 FFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKE 413 F NTMRL++ E+I GI + I+E Sbjct: 359 FDPQGTRNNTMRLSYCNNTPEEIERGIPIITRAIRE 394 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: 454 Number of extensions: 26 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: 417 Length of database: 397 Length adjustment: 31 Effective length of query: 386 Effective length of database: 366 Effective search space: 141276 Effective search space used: 141276 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 10 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