Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_123809439.1 BTUS_RS11380 acetylornithine transaminase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_000092905.1:WP_123809439.1 Length = 386 Score = 319 bits (817), Expect = 1e-91 Identities = 161/371 (43%), Positives = 227/371 (61%), Gaps = 4/371 (1%) Query: 29 VRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSNVFTNEPALR 88 VRG G +WD G + +DFA GIAV +LGH+HPA+ A+ +QA L H SN+F + Sbjct: 12 VRGEGVWLWDADGNQYLDFAAGIAVTILGHSHPAVAEAIADQARTLLHCSNLFYIPQQVE 71 Query: 89 LAHKLVDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTLFT 148 LA+ LV+ + ++VFFCNSG EA+EAA KLARR A+ E+ ++ +SFHGRTL Sbjct: 72 LANWLVNHSALDQVFFCNSGTEASEAAIKLARRWAYHNGVPERSTVITLEHSFHGRTLGA 131 Query: 149 VNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSDKTCAVVLEPIQGEGGVLPAELSY 208 + Q KY +GFGP + G+ HVP D+ AL+ A+ CAV++E +QGEGGV+P Y Sbjct: 132 LTATAQPKYQEGFGPLLGGVRHVPVGDVKALEEALDGTVCAVMMEMVQGEGGVMPVPTDY 191 Query: 209 LQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTSAKSLGGGFPIAAMLT 268 +Q R LCD N LLV DEVQTGMGR+G FAY+ +GV PDI T AK L G P+ A+L Sbjct: 192 VQEVRALCDRRNVLLVIDEVQTGMGRTGTFFAYEQFGVEPDICTLAKGLANGVPVGAVLA 251 Query: 269 TEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLNGVNAKHDKFKTRLEQIGEK 328 +A+ V G+HG+T+GGNPLA A A ++V+ + + + RL Sbjct: 252 KRPVAEAFVPGSHGSTFGGNPLAMRAALATVEVVEKERLWEKAARRGAYLRGRLANALGN 311 Query: 329 YGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNAAEREGLMILQAGPDVIRFAPSLVVEDAD 388 + F E+RG+GL++G VL + A + A + GL++ AG + +R P L+VE+ + Sbjct: 312 HPHFREIRGMGLMIGVVLDEG----ASQVAEACLKRGLLVTVAGGNTVRLLPPLIVEEPE 367 Query: 389 IDAGLDRFERA 399 ID ++R A Sbjct: 368 IDMAVERLSAA 378 Lambda K H 0.320 0.136 0.400 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: 396 Number of extensions: 19 Number of successful extensions: 2 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: 386 Length adjustment: 31 Effective length of query: 375 Effective length of database: 355 Effective search space: 133125 Effective search space used: 133125 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 Apr 10 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