Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_013451176.1 CALNI_RS05270 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_000183405.1:WP_013451176.1 Length = 459 Score = 118 bits (295), Expect = 4e-31 Identities = 112/415 (26%), Positives = 179/415 (43%), Gaps = 65/415 (15%) Query: 30 RGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSNVFTNEP-ALR 88 RG G +++D D N+ GH + + + Q N L HV P A+R Sbjct: 34 RGKGVKLYDIDNNYYYDTVSSWWTNIFGHNNKHINHKIRSQLNSLDHVIFAGMTHPYAVR 93 Query: 89 LAHKLVD--ATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTL 146 + L + R FF ++G+ A E A K+A + + EK + V NS+HG T+ Sbjct: 94 VVELLRNFLPEKLSRFFFSDNGSTAVEVAIKMAFQYWQNIGRVEKTKFVFFENSYHGDTI 153 Query: 147 FTVNVGGQSKYSDGFGPKITGITHVP----YNDLAALKAAV--SDKTC------------ 188 V+VGG Y + P + + YN + + + +D C Sbjct: 154 GAVSVGGIDLYHKLYKPLMFNSYQIRSPKCYNCIFSKQKMTLNADNGCNAECMDQLEKVL 213 Query: 189 --------AVVLEP-IQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLF 239 V++EP IQ G+ L+ RELCD + LL+FDEV TG GR+GK+F Sbjct: 214 EENNGNIAGVIIEPLIQCAAGMNVYNGIVLKKIRELCDRYEVLLIFDEVATGFGRTGKMF 273 Query: 240 AYQHYGVTPDILTSAKSLGGGF-PIAAMLTTEDLAKHLV-------VGTHGTTYGGNPLA 291 A++H V PDI+ +K L GG+ P+A +TTE++ HG +Y NP++ Sbjct: 274 AFEHVDVLPDIICLSKGLTGGYLPLALTVTTEEIYSAFYDDYFSYKTFFHGHSYTANPIS 333 Query: 292 CAVAEAVIDVINTPEVLNGVNAKHDKFKTRLEQIGEKY------GLFTEVRGLGLLLGCV 345 C+ A ++ N + K+K+ + EK +VR +G + Sbjct: 334 CSAAIGTLE--------NFIKKPIAKYKSGMIYFNEKVCSLKDEPYVGDVRYIGFIGAID 385 Query: 346 LSDAWKGKAKDIFNAAEREGL----------MILQAGPDVIRFAPSLVVEDADID 390 + + + GK+ + ER G +IL+ D I + + V+ DID Sbjct: 386 IVNPYTGKS---YPEKERVGFQIYKESLKNNLILRPLGDTIYWLLPITVKKKDID 437 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: 385 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 406 Length of database: 459 Length adjustment: 32 Effective length of query: 374 Effective length of database: 427 Effective search space: 159698 Effective search space used: 159698 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 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