Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_058932075.1 AU252_RS19120 ketol-acid reductoisomerase
Query= BRENDA::Q59818 (333 letters) >NCBI__GCF_001484605.1:WP_058932075.1 Length = 341 Score = 441 bits (1133), Expect = e-128 Identities = 215/332 (64%), Positives = 261/332 (78%) Query: 1 MAELFYDADADLSIIQGRKVAVIGYGSQGHAHALSLRDSGVDVRVGLHEGSKSKAKAEEQ 60 M E+FYD DADLSIIQGRKVA++GYGSQGHAHAL+LRDSGV+V + L EGSKS AKAEE Sbjct: 1 MTEMFYDDDADLSIIQGRKVAIVGYGSQGHAHALNLRDSGVEVVIALKEGSKSIAKAEEA 60 Query: 61 GLRVVTPSEAAAEADVIMILVPDPIQAQVYEESIKDNLKDGDALFFGHGLNIRFGFIKPP 120 G + +T ++AA ADVIMIL PD Q +Y +SIKD L G AL F HG NIRFG+I+ P Sbjct: 61 GFKALTVADAAEWADVIMILAPDQYQRSIYNDSIKDKLTPGKALAFAHGFNIRFGYIEAP 120 Query: 121 AGVDVCMVAPKGPGHLVRRQYEEGRGVPCIAAVEQDATGNGFALALSYAKGIGGTRAGVI 180 GVDV ++APK PGH VRR++E GRG+P I AVEQDATG + LA SYAK IGGTRAGVI Sbjct: 121 EGVDVILIAPKAPGHTVRREFEAGRGIPDIIAVEQDATGAAWDLAKSYAKAIGGTRAGVI 180 Query: 181 KTTFTEETETDLFGEQAVLCGGTAALVKAGFETLTEAGYQPEIAYFECLHELKLIVDLMY 240 KTTFTEETETDLFGEQ+VLCGG + LV+ GFETLTEAGYQP+IAYFE LHELKLIVDLM+ Sbjct: 181 KTTFTEETETDLFGEQSVLCGGVSQLVQYGFETLTEAGYQPQIAYFEVLHELKLIVDLMW 240 Query: 241 EGGLEKMRWSISETAEWGDYVTGPRIITDATKAEMKKVLAEIQDGTFAQAWMDEYHGGLK 300 EGG+ K RWS+S+TAE+GDYV+GPR+IT K M+ VLA+IQ G FA+ ++D+ G + Sbjct: 241 EGGIAKQRWSVSDTAEYGDYVSGPRVITPEVKENMQAVLADIQSGAFAKRFIDDQDNGGE 300 Query: 301 KYNEYKTQDENHLLETTGKELRKLMSWVNDEE 332 ++ + + E H +E G+ELR L +W +E Sbjct: 301 EFKALRAKAEQHPIEAVGRELRSLFAWQQTDE 332 Lambda K H 0.316 0.135 0.395 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: 403 Number of extensions: 15 Number of successful extensions: 1 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: 333 Length of database: 341 Length adjustment: 28 Effective length of query: 305 Effective length of database: 313 Effective search space: 95465 Effective search space used: 95465 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_058932075.1 AU252_RS19120 (ketol-acid reductoisomerase)
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00465.hmm # target sequence database: /tmp/gapView.17500.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00465 [M=314] Accession: TIGR00465 Description: ilvC: ketol-acid reductoisomerase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-130 421.2 0.2 1.2e-130 421.1 0.2 1.0 1 lcl|NCBI__GCF_001484605.1:WP_058932075.1 AU252_RS19120 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001484605.1:WP_058932075.1 AU252_RS19120 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 421.1 0.2 1.2e-130 1.2e-130 1 313 [. 15 328 .. 15 329 .. 0.99 Alignments for each domain: == domain 1 score: 421.1 bits; conditional E-value: 1.2e-130 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 ++g+kvai+GyGsqG+a+alnlrdsg++v+++l+++++s++kAee Gfk ltv++a++ ad+imiL pD lcl|NCBI__GCF_001484605.1:WP_058932075.1 15 IQGRKVAIVGYGSQGHAHALNLRDSGVEVVIALKEGSKSIAKAEEAGFKALTVADAAEWADVIMILAPD 83 6899***************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 + q++ y+ +ik++l+ gkal f+HGfni f +i++p++vdv+l+APK+pG++vR+e++ grG+p +iA lcl|NCBI__GCF_001484605.1:WP_058932075.1 84 QYQRSIYNDSIKDKLTPGKALAFAHGFNIRFGYIEAPEGVDVILIAPKAPGHTVRREFEAGRGIPDIIA 152 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 veqd+tg a + A++yAkaiGg+ragv++ttF eE+e+DLfGEq+vLcGg+++l++ +f+tL+eaGyqp lcl|NCBI__GCF_001484605.1:WP_058932075.1 153 VEQDATGAAWDLAKSYAKAIGGTRAGVIKTTFTEETETDLFGEQSVLCGGVSQLVQYGFETLTEAGYQP 221 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 ++Ayfe++helklivdl+ e+G+++ r +vs+tA++g++ ++ ++++ e+k++mq +l +iq+G fak lcl|NCBI__GCF_001484605.1:WP_058932075.1 222 QIAYFEVLHELKLIVDLMWEGGIAKQRWSVSDTAEYGDYVSGpRVITPEVKENMQAVLADIQSGAFAKR 290 ********************************************************************* PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkae 313 ++ ++ +g +f++ r k +++ ie vG+elr l+ ++ lcl|NCBI__GCF_001484605.1:WP_058932075.1 291 FIDDQDNGGEEFKALRAKAEQHPIEAVGRELRSLFAWQ 328 **********************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (341 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 5.10 // [ok]
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