Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate AZOBR_RS22505 AZOBR_RS22505 omega amino acid--pyruvate aminotransferase
Query= reanno::SB2B:6938540 (460 letters) >FitnessBrowser__azobra:AZOBR_RS22505 Length = 436 Score = 286 bits (731), Expect = 1e-81 Identities = 163/440 (37%), Positives = 239/440 (54%), Gaps = 21/440 (4%) Query: 20 HLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSIADAAYA 79 H PFT + + K R+I RAEG + WDA+G K+ D+++GLWC G+ R+ I++A Sbjct: 9 HWMPFTANREF-KANPRLIARAEGAWYWDAEGRKIYDSLSGLWCCGAGHSRREISEAVAR 67 Query: 80 QLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLRMVRRYWDL 139 Q+ L Y+ FQ H A +LA K+AS+ P ++ VFF SGSEA DT+L+M R YW L Sbjct: 68 QIAELD-YSPAFQFGHPAAFKLAHKLASMTPAGLDHVFFVNSGSEATDTSLKMARAYWRL 126 Query: 140 KGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQ--GDLPIPGIVHIDQPY-WFGEGRD 196 KG P+K +I R YHG G SLGG+G + + + H P F +G Sbjct: 127 KGQPAKTKLIGRSKGYHGVNFGGISLGGIGGNRKLFGSGVEADHLPHTLLPQNAFTKGL- 185 Query: 197 MSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIKRILEKYNI 256 PE G + A ALE + +AA I EP G+ GV+ PP Y ++ + +K+NI Sbjct: 186 --PEQ-GAELADALEELVALHDASNIAAVIVEPLAGSAGVLPPPKGYLQRLRALCDKHNI 242 Query: 257 LFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVADVLISDG 316 L I DEVI+GFGR G F A G+ PD++ +AKG+T+G +PMG V+ + + + +G Sbjct: 243 LLIFDEVITGFGRMGAAFGADAFGVVPDIMNVAKGLTNGAVPMGAVVANHEIYQTFMDNG 302 Query: 317 G-----EFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLSAHPL 371 G EF HG+TYS HPVA A L + + E ++L +K D P+ + L L Sbjct: 303 GADYMVEFPHGYTYSAHPVACAAGLAALELFERDKLAEKA-ADLAPHFETVLHGLKGLRH 361 Query: 372 VGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMIISPPLC 431 V ++R G+ GA+++ A R EI+ C ++G +R GDT+ P Sbjct: 362 VTDIRNYGLAGAVQIAALPGEPARRPYEIAM------KCWKAGFYVRFGGDTLQFGPHFI 415 Query: 432 ITRDEIDELIFKASQALSLT 451 R+++D L+ S A+ T Sbjct: 416 SEREDLDRLMNAVSDAIQAT 435 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: 532 Number of extensions: 24 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: 436 Length adjustment: 33 Effective length of query: 427 Effective length of database: 403 Effective search space: 172081 Effective search space used: 172081 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