Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 6938547 Sama_2650 methylmalonate-semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::G5CZI2 (498 letters) >FitnessBrowser__SB2B:6938547 Length = 496 Score = 634 bits (1634), Expect = 0.0 Identities = 304/498 (61%), Positives = 385/498 (77%), Gaps = 2/498 (0%) Query: 1 MTTIGHLINGQLVTENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTP 60 M +I H +NGQ + R+Q VF PATGE Q+ LAST+ V +AI+ A+ AF +W Sbjct: 1 MQSITHFVNGQHTAPSARTQTVFEPATGEARAQVSLASTQEVGEAIAVAKAAFESWSQMT 60 Query: 61 PLKRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKG 120 PL RAR++F+FK L+E + DE+ +LI EHGK+ DA GEL RG+E VE+ACG P LLKG Sbjct: 61 PLNRARILFKFKALVEANMDELAQLITREHGKVLDDAKGELIRGLEVVEFACGIPHLLKG 120 Query: 121 EHSRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSS 180 EH+ VG G+D+W+ QP+GVVAGI PFNFPVMVP+WMFP+AI CGN F++KPSE+DPSS Sbjct: 121 EHTAQVGTGVDAWAVNQPLGVVAGIAPFNFPVMVPMWMFPIAIACGNTFIMKPSEKDPSS 180 Query: 181 TLYIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANG 240 + IA+LL+EAGLPDGV NVVNGDKEAVD LL ++AVSFVGSTPIAEYIY TASA+G Sbjct: 181 VMRIAELLKEAGLPDGVFNVVNGDKEAVDTLLTHKDIQAVSFVGSTPIAEYIYATASAHG 240 Query: 241 KRCQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSK 300 KR QALGGAKNH ++MPDAD+D AVN L+GAA+GS+GERCMA+SV +AVGD AGDALV K Sbjct: 241 KRVQALGGAKNHMLLMPDADLDQAVNALMGAAYGSAGERCMAISVVLAVGD-AGDALVEK 299 Query: 301 MTQAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPNHEN 360 + + LKVG + GP+I+ QH +KV Y+ + ++GA+++VDGR+ + + N Sbjct: 300 LLPKIAALKVGNGLIPDMEMGPLISAQHLDKVSSYVEAGVREGASLLVDGRELSMEDKAN 359 Query: 361 GFFVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGE 420 G+F+G L DHVTP+M+ Y+EEIFGPVL +VRV A+ LI+ HE+GNGT IFT+ GE Sbjct: 360 GYFLGACLFDHVTPQMSIYKEEIFGPVLSIVRVPDYNSALQLINDHEFGNGTAIFTQSGE 419 Query: 421 AARYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQR 480 AAR+F ++QVGMVG+N+P+PVP+A+HSFGGWKRSLFG LH +GPD VRFYTKRK +T R Sbjct: 420 AARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAITAR 479 Query: 481 WPSAGVREGAEFSMPTMK 498 WP G + AEF MPTMK Sbjct: 480 WPQ-GKQLAAEFVMPTMK 496 Lambda K H 0.319 0.135 0.405 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: 727 Number of extensions: 24 Number of successful extensions: 3 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: 498 Length of database: 496 Length adjustment: 34 Effective length of query: 464 Effective length of database: 462 Effective search space: 214368 Effective search space used: 214368 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 (21.7 bits) S2: 52 (24.6 bits)
Align candidate 6938547 Sama_2650 (methylmalonate-semialdehyde dehydrogenase (RefSeq))
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))
# 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.carbon/TIGR01722.hmm # target sequence database: /tmp/gapView.3270700.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01722 [M=477] Accession: TIGR01722 Description: MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating) 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-210 684.2 0.6 5.2e-210 684.0 0.6 1.0 1 FitnessBrowser__SB2B:6938547 Domain annotation for each sequence (and alignments): >> FitnessBrowser__SB2B:6938547 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 684.0 0.6 5.2e-210 5.2e-210 2 477 .] 5 480 .. 4 480 .. 0.99 Alignments for each domain: == domain 1 score: 684.0 bits; conditional E-value: 5.2e-210 TIGR01722 2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrdeiak 82 h+++G+ + s++ v +pat+e a+v+ as++ev +a+a a+ +f +w++ + ++rar+l++++al++++ de+a+ FitnessBrowser__SB2B:6938547 5 THFVNGQHT-APSARTQTVFEPATGEARAQVSLASTQEVGEAIAVAKAAFESWSQMTPLNRARILFKFKALVEANMDELAQ 84 688888875.56788899*************************************************************** PP TIGR01722 83 lisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamiplwmfplaiac 163 li+ e+Gk+l+dakG+++rGlevve+ac+++ ll+Ge + +v + vd ++++qplGvvaGi+pfnfp m+p+wmfp+aiac FitnessBrowser__SB2B:6938547 85 LITREHGKVLDDAKGELIRGLEVVEFACGIPHLLKGEHTAQVGTGVDAWAVNQPLGVVAGIAPFNFPVMVPMWMFPIAIAC 165 ********************************************************************************* PP TIGR01722 164 GntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqal 244 Gntf++kpsek+ps+ +++aell+eaG+pdGv+nvv Gdkeavd+ll h d++avsfvGs++++eyiy t+sahgkrvqal FitnessBrowser__SB2B:6938547 166 GNTFIMKPSEKDPSSVMRIAELLKEAGLPDGVFNVVNGDKEAVDTLLTHKDIQAVSFVGSTPIAEYIYATASAHGKRVQAL 246 ********************************************************************************* PP TIGR01722 245 aGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.kelveeireraekvrvgagddpgaelGplitkqa 324 +Gaknhm+++pdad+++a++al+gaa+G+aG+rcmais++++vG+a + lve++ +++ ++vg g p e+Gpli+ q+ FitnessBrowser__SB2B:6938547 247 GGAKNHMLLMPDADLDQAVNALMGAAYGSAGERCMAISVVLAVGDAgDALVEKLLPKIAALKVGNGLIPDMEMGPLISAQH 327 **********************************************999******************************** PP TIGR01722 325 kervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyG 405 ++v+s++++g++eGa++l+dGr + +e +G f+G +l+++v p+m+iykeeifGpvl ++++ ++ a++lin+ +G FitnessBrowser__SB2B:6938547 328 LDKVSSYVEAGVREGASLLVDGRELSMEDKANGYFLGACLFDHVTPQMSIYKEEIFGPVLSIVRVPDYNSALQLINDHEFG 408 ********************************************************************************* PP TIGR01722 406 nGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477 nGtaift++G aar+f h+++vG+vGvnvpipvp++f+sf+Gwk slfG lh++G +Gvrfyt+ k++tarw FitnessBrowser__SB2B:6938547 409 NGTAIFTQSGEAARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAITARW 480 ************************************************************************ PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (477 nodes) Target sequences: 1 (496 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 18.56 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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