Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF919 PGA1_c09350 aminotransferase class-III
Query= BRENDA::A0A140N9B6 (406 letters) >FitnessBrowser__Phaeo:GFF919 Length = 450 Score = 154 bits (389), Expect = 5e-42 Identities = 125/416 (30%), Positives = 193/416 (46%), Gaps = 44/416 (10%) Query: 27 RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASK--FWHTGNGYTNEPVL 84 RGEG ++D G++YI+ G+ +LG+++ E+ +A+ EQ K F HT G T++P+ Sbjct: 21 RGEGIYVFDSDGRKYIEGLAGLWCTSLGYSNTEVMDAITEQLHKLPFTHTFGGKTHQPIQ 80 Query: 85 RLAKKLIDATFADR--VFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHGRT 142 LA KL + +FF NSG++AN+ K+ R + + K I+ + +HG T Sbjct: 81 DLADKLAAMVPVEDAYIFFGNSGSDANDTHYKMLRYYFNAIGKPEKRKIITRERGYHGVT 140 Query: 143 LFTVSAGGQPAYSQDF-APLPA------DIRH--AAYNDINSASALID------------ 181 + S PA F APL A D H A + + ++ Sbjct: 141 VAAGSLTSLPANLAHFDAPLEALSILRADSPHYYTARQGNETEAQFVERILQNLEDQIIS 200 Query: 182 ---DSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAY 238 D+ A+IVEPI G GV+ + + +GL+ L ++ L+ DEV G GRTG + Sbjct: 201 EDPDTIAAMIVEPITGASGVIVPPDGYYEGLQALLRKYGILIWADEVICGFGRTGADFGC 260 Query: 239 MHYGVTPDLLTTAKALGGG-FPVGALL-------ATEECARVMTVGTHGTTYGGNPLASA 290 G+TPDL+T AK L FP+ A + A + + V HG TY G+P A A Sbjct: 261 TTMGITPDLMTFAKQLSSAYFPISASVIPGWMYEAMVDQTNEVGVFGHGYTYSGHPAACA 320 Query: 291 VAGKVLELINTPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYA-- 348 A K LE+ + + + + +L I + L EVRG GL+ L ++ Sbjct: 321 AALKTLEIYERDNLFDHAAEVGSYLQTQLREIFTDHPLVGEVRGKGLIAALELVSNKTTG 380 Query: 349 -----GQAKQISQEAAKAGVMVLIA-GGNVVRFAPALNVSEEEVTTGLDRFAAACE 398 G+A +Q + ++L A GN V P L ++ EEV L R A + Sbjct: 381 ASFDKGRAGATAQRLCQDNGLILRAVAGNAVALCPPLIITREEVDDMLTRLKTAID 436 Lambda K H 0.319 0.135 0.406 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: 450 Number of extensions: 27 Number of successful extensions: 6 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: 406 Length of database: 450 Length adjustment: 32 Effective length of query: 374 Effective length of database: 418 Effective search space: 156332 Effective search space used: 156332 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 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