Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate BPHYT_RS30220 BPHYT_RS30220 hypothetical protein
Query= reanno::SB2B:6938540 (460 letters) >FitnessBrowser__BFirm:BPHYT_RS30220 Length = 465 Score = 346 bits (888), Expect = e-100 Identities = 195/456 (42%), Positives = 268/456 (58%), Gaps = 11/456 (2%) Query: 9 ISALQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGY 68 I +L D H +HP + RG V+E A G ++ DA GN+LLDA +GLWCVNVGY Sbjct: 3 IQSLIEADRKHLIHPVINYRAHEARGVTVLESASGAFLRDAAGNELLDAFSGLWCVNVGY 62 Query: 69 GRKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDT 128 G++SI DAA AQ+Q LP+ +F EPAI LA K+ ++P + V+FT GS+A D+ Sbjct: 63 GQQSIVDAATAQMQKLPYATGYFHFGSEPAIELAQKLVEVSPASLQHVYFTLGGSDAVDS 122 Query: 129 NLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQP 188 LR + Y++ G PSKK II+ + YHGS+ GA L + H+ DLP+P H+ P Sbjct: 123 ALRFITHYFNSTGRPSKKHIIALQRGYHGSSTTGAGLTALPAFHRNFDLPLPNQHHLPSP 182 Query: 189 YWFGEGRDMSPEAFGI-KTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEI 247 Y + D + +A I + ALEAK+ ELG D VAAF EP QG+GGVI+PP + + Sbjct: 183 YAY--RNDFADDAALIAASVAALEAKVAELGADNVAAFFCEPIQGSGGVIVPPVGWLKAM 240 Query: 248 KRILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDR 307 + K ILF+ DEVI+GFGRTG FA Q ++PDL+T+AKG+T+GY PMG V++SD Sbjct: 241 RESCRKLGILFVADEVITGFGRTGPLFACQGENVEPDLMTVAKGLTAGYAPMGAVLMSDE 300 Query: 308 VADVLISDGGE--FAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQT 365 + + E HG TYS HPV+AA+ LE +R+ E L+ P L Sbjct: 301 IYQGIADSHAEAVVGHGHTYSAHPVSAAIGLEVLRLYHEGGLLAN-GVARAPRFARGLDA 359 Query: 366 LSAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMI 425 L AHPLVG+ R G++GA+ELVADK S F + A E+ L+ RA GD ++ Sbjct: 360 LLAHPLVGDSRHRGLLGALELVADKDSKAGFDPALKLSERIAAAAYENRLIFRAFGDNIL 419 Query: 426 -ISPPLCITRDEIDELIFKASQALSLTLEKIAARGN 460 +P L T E D L+F + L TL+ + A+ + Sbjct: 420 GFAPALSYTEAEFD-LMF---ERLEKTLDDVLAQAD 451 Lambda K H 0.321 0.137 0.408 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: 551 Number of extensions: 18 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: 460 Length of database: 465 Length adjustment: 33 Effective length of query: 427 Effective length of database: 432 Effective search space: 184464 Effective search space used: 184464 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 (21.8 bits) S2: 51 (24.3 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