Align arginosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate N515DRAFT_3770 N515DRAFT_3770 argininosuccinate lyase
Query= reanno::Dyella79:N515DRAFT_3770 (433 letters) >FitnessBrowser__Dyella79:N515DRAFT_3770 Length = 433 Score = 848 bits (2190), Expect = 0.0 Identities = 433/433 (100%), Positives = 433/433 (100%) Query: 1 MTQPLWQKSGIQIDARIMRFLAGDDVVLDREFFLHDITASKAHVEGLAKIGVVSADEAAA 60 MTQPLWQKSGIQIDARIMRFLAGDDVVLDREFFLHDITASKAHVEGLAKIGVVSADEAAA Sbjct: 1 MTQPLWQKSGIQIDARIMRFLAGDDVVLDREFFLHDITASKAHVEGLAKIGVVSADEAAA 60 Query: 61 LKRELDALAADFSAGDFVLDESYEDGHSAIEARLTERLGDAGRRVHTGRSRNDQILVATR 120 LKRELDALAADFSAGDFVLDESYEDGHSAIEARLTERLGDAGRRVHTGRSRNDQILVATR Sbjct: 61 LKRELDALAADFSAGDFVLDESYEDGHSAIEARLTERLGDAGRRVHTGRSRNDQILVATR 120 Query: 121 LWLKDQLAVLETHCRAIAEVCLERAAQPALPLPGYTHIQRAVVSSTAMWFAGFAEGFIDN 180 LWLKDQLAVLETHCRAIAEVCLERAAQPALPLPGYTHIQRAVVSSTAMWFAGFAEGFIDN Sbjct: 121 LWLKDQLAVLETHCRAIAEVCLERAAQPALPLPGYTHIQRAVVSSTAMWFAGFAEGFIDN 180 Query: 181 TLRARQTAALIDCNPLGTAAGYGVNLPLDREHTTQALGFARMQVSPVYAQLSRGKFEMAV 240 TLRARQTAALIDCNPLGTAAGYGVNLPLDREHTTQALGFARMQVSPVYAQLSRGKFEMAV Sbjct: 181 TLRARQTAALIDCNPLGTAAGYGVNLPLDREHTTQALGFARMQVSPVYAQLSRGKFEMAV 240 Query: 241 LEAIAAALLDVRRLAWDLSLFTTAEFGFVKLPSEYTTGSSIMPNKRNPDVVELLRASYAS 300 LEAIAAALLDVRRLAWDLSLFTTAEFGFVKLPSEYTTGSSIMPNKRNPDVVELLRASYAS Sbjct: 241 LEAIAAALLDVRRLAWDLSLFTTAEFGFVKLPSEYTTGSSIMPNKRNPDVVELLRASYAS 300 Query: 301 VAAARTEIEQLLSLPSGYQRDLQFSKGSLFHGCRHGLAALELVPDLLARMEWHEPAMRAA 360 VAAARTEIEQLLSLPSGYQRDLQFSKGSLFHGCRHGLAALELVPDLLARMEWHEPAMRAA Sbjct: 301 VAAARTEIEQLLSLPSGYQRDLQFSKGSLFHGCRHGLAALELVPDLLARMEWHEPAMRAA 360 Query: 361 IEPAMYATDVAIEQAAAGVPFRDAYRAAADAAASAGAGRTPEGSLAARVSPGAGHDLRLD 420 IEPAMYATDVAIEQAAAGVPFRDAYRAAADAAASAGAGRTPEGSLAARVSPGAGHDLRLD Sbjct: 361 IEPAMYATDVAIEQAAAGVPFRDAYRAAADAAASAGAGRTPEGSLAARVSPGAGHDLRLD 420 Query: 421 ELKARLAALTPGH 433 ELKARLAALTPGH Sbjct: 421 ELKARLAALTPGH 433 Lambda K H 0.320 0.133 0.388 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: 793 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: 433 Length of database: 433 Length adjustment: 32 Effective length of query: 401 Effective length of database: 401 Effective search space: 160801 Effective search space used: 160801 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 (21.9 bits) S2: 51 (24.3 bits)
Align candidate N515DRAFT_3770 N515DRAFT_3770 (argininosuccinate lyase)
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))
# 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/TIGR00838.hmm # target sequence database: /tmp/gapView.8204.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00838 [M=455] Accession: TIGR00838 Description: argH: argininosuccinate lyase 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-87 281.0 0.0 1.3e-87 280.6 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_3770 N515DRAFT_3770 argininosuccinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_3770 N515DRAFT_3770 argininosuccinate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 280.6 0.0 1.3e-87 1.3e-87 20 391 .. 25 393 .. 11 402 .. 0.95 Alignments for each domain: == domain 1 score: 280.6 bits; conditional E-value: 1.3e-87 TIGR00838 20 slsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevdaeDiHlav 85 + D e++ +Di++s+ah++ Lak g+++++ea+ l+++L+ l+ + ++g++ l++++eD H+a+ lcl|FitnessBrowser__Dyella79:N515DRAFT_3770 25 DVVLDREFFLHDITASKAHVEGLAKIGVVSADEAAALKRELDALAADFSAGDFVLDESYEDGHSAI 90 56789************************************************************* PP TIGR00838 86 ErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpg 151 E++l++++g d+g+++htgrsRnDq+ + rl+l+d++ l ++ +++ ++ +e+A++ +pg lcl|FitnessBrowser__Dyella79:N515DRAFT_3770 91 EARLTERLG-DAGRRVHTGRSRNDQILVATRLWLKDQLAVLETHCRAIAEVCLERAAQP-ALPLPG 154 *********.**********************************************987.7889** PP TIGR00838 152 ytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFd 217 ytH+qrA + a ++ +ae + ++ R ++ ++ +PlG++A g+++++dre +++ LgF+ lcl|FitnessBrowser__Dyella79:N515DRAFT_3770 155 YTHIQRAVVSSTAMWFAGFAEGFIDNTLRARQTAALIDCNPLGTAAGYGVNLPLDREHTTQALGFA 220 ****************************************************************** PP TIGR00838 218 avvensldavsdR.DfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKK 282 ++ ++a +R f + +l a+a + +++ rla +l lf+++Efgfv+l+ e+++gssimP K+ lcl|FitnessBrowser__Dyella79:N515DRAFT_3770 221 RMQVSPVYAQLSRgKFEMAVLEAIAAALLDVRRLAWDLSLFTTAEFGFVKLPSEYTTGSSIMPNKR 286 **9999999766637999************************************************ PP TIGR00838 283 npDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelk 348 npDv+El+R+ + v+ t + l +lP+ Y++Dlq k +lf ++ +le+v ll+ ++ lcl|FitnessBrowser__Dyella79:N515DRAFT_3770 287 NPDVVELLRASYASVAAARTE-IEQLLSLPSGYQRDLQFSKGSLFHGCRHGLAALELVPDLLARME 351 ***************988665.677889************************************** PP TIGR00838 349 vnkerleeaakknfalatdlAdylvrkGvPFReaheivGevva 391 ++ ++aa + + atd+A ++ GvPFR+a++ + +++a lcl|FitnessBrowser__Dyella79:N515DRAFT_3770 352 WHEPA-MRAAIEPAMYATDVAIEQAAAGVPFRDAYRAAADAAA 393 *9888.899999************************9987766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (433 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8.19 // [ok]
This GapMind analysis is from Apr 09 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