Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_017751620.1 PN53_RS13955 branched-chain amino acid transaminase
Query= BRENDA::F2L0W0 (295 letters) >NCBI__GCF_000816635.1:WP_017751620.1 Length = 304 Score = 266 bits (680), Expect = 4e-76 Identities = 137/299 (45%), Positives = 191/299 (63%), Gaps = 6/299 (2%) Query: 3 VWLDGRLVDEEEAKVTVLSPSLNYGFGVFEGIRAYWNGEN--LYVFRLRDHMERLLRSAK 60 V+ G++VDE E + + S + NYG G FEGIRAYW+ E L+ FRL+DH RLL+S+K Sbjct: 6 VFYQGKIVDESEVTIGIRSKAFNYGLGCFEGIRAYWDEEQKQLFGFRLKDHYTRLLQSSK 65 Query: 61 IIGLDVPYTAEELSKAVVETVRANGFKEDLYIRPVAYISKPQISLDVRGLQASVAIAAIP 120 + L++PYTA+ELSK +E ++ N K YIRP+ Y I ++ V I P Sbjct: 66 SLNLNIPYTADELSKWTIELLKKNNCKRTTYIRPIVYNDAQDIGPNLSKPDTKVVIYCQP 125 Query: 121 FGKYLKVEGVRAAVVSWRRVHTSMMPVMAKATGIYLNSIMAAVEARARGYDEAIMLNAEG 180 KY + + SWRR+ +M+P KAT YLNS +A++EA+ G+DEAI L + Sbjct: 126 LDKYAGKSELSVGITSWRRLEDNMLPPRTKATAAYLNSALASLEAKRAGFDEAIFLTSGN 185 Query: 181 KVVEGSGENIFIVRRGVLMTPPLEDGILEGITRETVISIA-GDLGIPLLEKSITREELYA 239 V EG GENIFI ++G L+TPP D ILEGITR+ V+ + +LG+ + E+SI R ELYA Sbjct: 186 HVCEGPGENIFIYKKGKLITPPASDNILEGITRDLVMQLGKEELGLEVQERSIARTELYA 245 Query: 240 ADEAFFVGTAAEITPIIEIDGRVL---QRGPITQKIAETYRRIVLGKEEKYLPWLTPVY 295 +DE FF GTA E+TPIIE+D RV+ ++G + +KI E + + +GK KY + TPVY Sbjct: 246 SDEVFFSGTAMEVTPIIEVDHRVVGDGKQGEVCKKIKELFFNLTVGKNPKYAHYCTPVY 304 Lambda K H 0.320 0.138 0.396 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: 272 Number of extensions: 7 Number of successful extensions: 4 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: 295 Length of database: 304 Length adjustment: 27 Effective length of query: 268 Effective length of database: 277 Effective search space: 74236 Effective search space used: 74236 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: 48 (23.1 bits)
Align candidate WP_017751620.1 PN53_RS13955 (branched-chain amino acid transaminase)
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))
# 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/TIGR01122.hmm # target sequence database: /tmp/gapView.1877881.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01122 [M=298] Accession: TIGR01122 Description: ilvE_I: branched-chain amino acid aminotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-100 319.8 0.0 9.3e-100 319.6 0.0 1.0 1 NCBI__GCF_000816635.1:WP_017751620.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000816635.1:WP_017751620.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 319.6 0.0 9.3e-100 9.3e-100 1 298 [] 7 303 .. 7 303 .. 0.96 Alignments for each domain: == domain 1 score: 319.6 bits; conditional E-value: 9.3e-100 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglai..frlkehveRlydsakilrleipyskeelv 71 +++G++vd+ + ++ + ++a+ YG g feGiRaY+ ++++++ frlk+h+ Rl++s+k+l+l+ipy+++el+ NCBI__GCF_000816635.1:WP_017751620.1 7 FYQGKIVDESEVTIGIRSKAFNYGLGCFEGIRAYWDEEQKQLfgFRLKDHYTRLLQSSKSLNLNIPYTADELS 79 789*******************************998866652379*************************** PP TIGR01122 72 evtkevlrknnlks.aYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraav 143 + t+e+l+knn k +YiRp+vy a+d+g + ++ +++v+i+ ++ +y g+ l+ G ++s+rr ++ NCBI__GCF_000816635.1:WP_017751620.1 80 KWTIELLKKNNCKRtTYIRPIVYNDAQDIGPNL-SKPDTKVVIYCQPLDKYAGKSELSVG----ITSWRRLED 147 ************9889*************9988.8889***************9766666....579****** PP TIGR01122 144 nsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrda 216 n++p+++ka+++Ylns+la ea+raG+deai+L + +v eG+Genifi k+g+l+tPp s++iL+gitrd NCBI__GCF_000816635.1:WP_017751620.1 148 NMLPPRTKATAAYLNSALASLEAKRAGFDEAIFLTSGNHVCEGPGENIFIYKKGKLITPPASDNILEGITRDL 220 ************************************************************************* PP TIGR01122 217 viklak.elgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegkt 288 v++l k elg+ev+e++i+r+ely +Devf++Gta evtPi evD+r +g+gk+G+v kk++e ff+l+ gk+ NCBI__GCF_000816635.1:WP_017751620.1 221 VMQLGKeELGLEVQERSIARTELYASDEVFFSGTAMEVTPIIEVDHRVVGDGKQGEVCKKIKELFFNLTVGKN 293 ****98689**************************************************************** PP TIGR01122 289 ekkeewltyv 298 +k++++ t+v NCBI__GCF_000816635.1:WP_017751620.1 294 PKYAHYCTPV 303 ****998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (304 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 13.02 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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