Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate SM_b21186 SM_b21186 4-aminobutyrate aminotransferase
Query= SwissProt::Q8ZPV2 (408 letters) >FitnessBrowser__Smeli:SM_b21186 Length = 422 Score = 231 bits (588), Expect = 4e-65 Identities = 149/395 (37%), Positives = 209/395 (52%), Gaps = 39/395 (9%) Query: 27 RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTN-EPALR 85 R E + +WD++G YIDFA GIAV GH HP + A+ Q +RF H + E + Sbjct: 26 RAENAEIWDKEGNRYIDFAAGIAVVNTGHRHPKVIAAVKAQLDRFTHTCHQVVPYENYVH 85 Query: 86 LAKKL---IDATFAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHGRT 142 LA++L + FA++ F +GAEA E A+K+AR + +VAF FHGRT Sbjct: 86 LAERLNAIVPGDFAKKTIFVTTGAEAVENAVKIAR------AATGRQAVVAFGGGFHGRT 139 Query: 143 LFTVSAGGQPT-YSQDFAPLPPDIRHAAYN-DLN------SASAL-------IDD-NTCA 186 ++ G+ Y F +P D+ HA + +L+ S SAL +D A Sbjct: 140 FMGMALTGKVVPYKVGFGAMPADVFHAPFPIELHGVTVEQSLSALKKLFAADVDPARVAA 199 Query: 187 VIVEPVQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPD 246 +I+EPVQGEGG P AF++ LRE+CD+H LLI DEVQTG RTG+L+A H+GV PD Sbjct: 200 IIIEPVQGEGGFYPVPTAFMKALREVCDQHGILLIADEVQTGFARTGKLFAMEHHGVAPD 259 Query: 247 ILTTAKALGGGFPIGAMLTTQDYASVMTPGTHGTTYGGNPLATAVAGKVLDIINTPEMQN 306 + T AK+L GGFP+ A+ + PG G TYGGNPL A A VLD+I + Sbjct: 260 LTTMAKSLAGGFPLAAVTGRAEIMDAPGPGGLGGTYGGNPLGIAAAHAVLDVIAEENLCE 319 Query: 307 GVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGC--------VLQTEFAGKAKLIAQEA 358 Q + +RL + + +IRG G + + EFA K +L+A E Sbjct: 320 RANQLGNRLKQRLAAIREKAPEIVDIRGPGFMNAVEFNDVRTNLPSAEFANKVRLLALE- 378 Query: 359 AKAGVMVLIAG--GDVVRFAPALNVSDEEIATGLD 391 G+++L G G+V+RF + + DE A LD Sbjct: 379 --KGLILLTCGVHGNVIRFLAPITIQDEVFAEALD 411 Lambda K H 0.320 0.137 0.413 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: 494 Number of extensions: 27 Number of successful extensions: 5 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: 408 Length of database: 422 Length adjustment: 31 Effective length of query: 377 Effective length of database: 391 Effective search space: 147407 Effective search space used: 147407 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