Align succinylornithine transaminase; EC 2.6.1.81 (characterized)
to candidate 6939514 Sama_3606 aminotransferase, class III; 4-aminobutyrate aminotransferase (RefSeq)
Query= CharProtDB::CH_002469 (406 letters) >FitnessBrowser__SB2B:6939514 Length = 472 Score = 156 bits (395), Expect = 1e-42 Identities = 132/409 (32%), Positives = 191/409 (46%), Gaps = 50/409 (12%) Query: 27 RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEPVLRL 86 R +GS +WD +YIDF G A N G+AHPE+ EA++ +++ G Y L Sbjct: 56 RAQGSFVWDLDDNQYIDFQNGWASNPFGNAHPEIVEAVHWAHTRY---GFHYDTPHRYEL 112 Query: 87 AKKLIDA---TFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHGRTL 143 A+KL+ R+ F SG EA EAA+ LA RY I++F ++FHG L Sbjct: 113 AEKLVQIMPNRALTRINFEISGTEAAEAAVNLALTHTKRRY------IISFSSSFHGEAL 166 Query: 144 FTVSAGG-------QPAYSQDF--AP------LPADIRHAAY---------NDINSASAL 179 + G A+S AP +PA + Y N I S S + Sbjct: 167 GSKMLSGTSNNNHYMEAWSGGVITAPYPYSGEIPAGMTQEQYVEYCLWYIDNHITS-SIV 225 Query: 180 IDDSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYM 239 ++ +I+EP EGG F+QGLRELCN+H+ ++I DEV TG+GRTG+++A Sbjct: 226 PANNIAGLIIEPGLAEGGNWIPPKRFMQGLRELCNKHDWVMIVDEVLTGLGRTGKMWAIE 285 Query: 240 HYGVTPDLLTTAKALGGGF-PVGALLATEECARVMTVGTH---GTTYGGNPLASAVAGKV 295 HY V PD+L K + GG P + A +E +M H G+TY G+P A K Sbjct: 286 HYDVIPDVLVFGKNISGGIEPCAGIAARDE---IMGDNEHYHTGSTYAGSPAACCAGLKT 342 Query: 296 LELINTPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQ----- 350 LEL ++ V + + + RY + +EVR GLL+G + Q Sbjct: 343 LELYERENIVEYVAYLGE-IAKGIMQKWTRYSIVNEVRCNGLLLGVNFVSPDEHQKDWWF 401 Query: 351 AKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEEEVTTGLDRFAAACEH 399 A+++ + GV + VR PALN+ E + GL A H Sbjct: 402 AREVRSRMMENGVWAINDRQTNVRLYPALNMEESVLREGLAIMEEAIAH 450 Lambda K H 0.319 0.136 0.407 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: 475 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 406 Length of database: 472 Length adjustment: 32 Effective length of query: 374 Effective length of database: 440 Effective search space: 164560 Effective search space used: 164560 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 Jul 25 2024. The underlying query database was built on Jul 25 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