Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 5207773 Shew_0294 alanine--glyoxylate transaminase (RefSeq)
Query= BRENDA::P21549 (392 letters) >FitnessBrowser__PV4:5207773 Length = 380 Score = 274 bits (700), Expect = 4e-78 Identities = 154/383 (40%), Positives = 220/383 (57%), Gaps = 7/383 (1%) Query: 7 LVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQY 66 ++ PK + P + P ++L+GPGPS++ P ++AA IG + +MDE+K IQY Sbjct: 1 MLAAPK--VTPFNPPRRVLMGPGPSDVYPEVLAAQARPTIGHLDPLFVGMMDELKSLIQY 58 Query: 67 VFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPM 126 FQT N +TL +S G +E VN++EPG+ +V NG++G+R ER+GA + Sbjct: 59 AFQTENAMTLAVSAPGSAGMETCFVNLVEPGEKVIVCRNGVFGERMRQNVERVGATAVVV 118 Query: 127 TKDPGGHYTLQEVEEGLAQHKPV-LLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSV 185 + G +L +VE L H L H E+STG L G +L + CL +VD+V Sbjct: 119 DNEWGTPVSLSDVEAALKAHPDAKFLAFVHAETSTGALSDAKGLCQLAKAHDCLSIVDAV 178 Query: 186 ASLGGTPLYMDRQGIDILYSGSQKALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIK 245 SLGG L +D GID +YSGSQK L+ PG S +SFS A +K+ +RKT S++LD Sbjct: 179 TSLGGVELRVDEWGIDAIYSGSQKCLSCVPGLSPVSFSPAAVEKLKARKTPVQSWFLDQS 238 Query: 246 WLANFWGCDD---QPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRL 302 + +W D R YHHT PV +LY+L ESL L+AE+GLEN+W +H A L L Sbjct: 239 LVMGYWSGDQGAGGKRSYHHTAPVNALYALHESLRLLAEEGLENAWARHHSMHALLRDGL 298 Query: 303 QALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIG 362 + LGL+ FV + RLP + V +P G D + +++++++EI GLG GK RIG Sbjct: 299 ENLGLK-FVVEEGSRLPQLNAVYIPEGVDDGAVRKQLLENYNLEIGAGLGALAGKAWRIG 357 Query: 363 LLGCNATRENVDRVTEALRAALQ 385 L+G A RENV AL L+ Sbjct: 358 LMGFGARRENVALCLRALEEVLR 380 Lambda K H 0.320 0.138 0.421 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: 378 Number of extensions: 17 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: 392 Length of database: 380 Length adjustment: 30 Effective length of query: 362 Effective length of database: 350 Effective search space: 126700 Effective search space used: 126700 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: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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