Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_012674645.1 SULAZ_RS07270 citramalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000021545.1:WP_012674645.1 Length = 533 Score = 248 bits (632), Expect = 5e-70 Identities = 172/519 (33%), Positives = 283/519 (54%), Gaps = 33/519 (6%) Query: 1 MPDRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGE---FEA 57 M +V I+DTTLRDG Q GVS++VE+K+ IA KL +FGV IE G+P ++ + F+ Sbjct: 1 MEKQVLIYDTTLRDGTQAEGVSVSVEDKLRIAEKLADFGVHYIEGGWPGSNPKDMTFFKE 60 Query: 58 VRAIAGEELDAEICGLARC----VKGD--IDAAIDADVDCVHVFIATSDIHLRYKLEMSR 111 V+ + + G R V+ D I I A+ + +F + D+H+ L+ + Sbjct: 61 VKKLNLKNTKITAFGSTRRSSLKVEEDPQIQDLIKAETPVITIFGKSWDLHVTQALKTTL 120 Query: 112 EEALERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTV 168 E+ LE + + Y + V F AE D + + DY +EV K + GAD + + DT Sbjct: 121 EKNLEMIYDSISYLKKYVDEVIFDAEHFFDGFKENPDYAIEVLKVAQQGGADFLILCDTN 180 Query: 169 GVMTPPEMYRLTAEVVDA-VDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGER 227 G P ++ + V +A + + +H HND AV NS+ AV GA QVH T+NGIGER Sbjct: 181 GGSLPTDIEKAFKAVKEAGITAKLGIHAHNDSDTAVWNSIVAVLHGAIQVHGTINGIGER 240 Query: 228 AGNASLEQVV--MALKALYDIELDVRTEMLVELSRLVERLTGVVVPPNTPIVGENAFAHE 285 GNA+L ++ ++LK Y+ + L E+S V + + VP N P VG++AFAH+ Sbjct: 241 CGNANLCSIIPNLSLKLGYETVPRENIKRLKEISNFVSDILNMPVPKNMPYVGDSAFAHK 300 Query: 286 SGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTE--EQLDE 343 G+H+ V++ +YE I P++VG+RR++++ AG+ I K +E+GIE+ E E+L + Sbjct: 301 GGVHASAVLRNPRSYEHILPQEVGNRRKVLVSDLAGKSNIIYKAKEIGIEIDEKDERLTK 360 Query: 344 IVRRVKELGDKGK--RVTEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNKFT-----P 396 +V+ +KEL ++G E LE + R +G +P+ L+ V+ ++T Sbjct: 361 LVQEIKELENQGYHFEAAEASLELLIRKHLGTLPK---YFDLDAYRVLIARRYTDKSPIS 417 Query: 397 TASVRVYLDGEEHEAASTGVGSVDAAIRALREAIEELG---MDVELKEYRLEAI--TGGT 451 A+VR+ ++ AS G G V+A +AL++A+ + +VEL +Y++ + +GGT Sbjct: 418 EATVRIKIENHYEHTASLGYGPVNALDKALKKALTAVYPSLAEVELIDYKVRIVNESGGT 477 Query: 452 DALAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGV 490 A V + D+ T G +++I+ AS +A V + Sbjct: 478 AAKIRVLIESRDKSKKWGTV-GVSDNIIEASWQAVVDSI 515 Lambda K H 0.315 0.133 0.364 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: 514 Number of extensions: 24 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: 499 Length of database: 533 Length adjustment: 35 Effective length of query: 464 Effective length of database: 498 Effective search space: 231072 Effective search space used: 231072 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 bits) S2: 52 (24.6 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