Align candidate WP_013553448.1 NITSA_RS02460 (methionine synthase)
to HMM PF02965 (Met_synt_B12)
# 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/PF02965.21.hmm # target sequence database: /tmp/gapView.24836.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Met_synt_B12 [M=273] Accession: PF02965.21 Description: Vitamin B12 dependent methionine synthase, activation domain 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-36 112.2 0.0 3.2e-36 111.2 0.0 1.5 1 lcl|NCBI__GCF_000186245.1:WP_013553448.1 NITSA_RS02460 methionine synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013553448.1 NITSA_RS02460 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 111.2 0.0 3.2e-36 3.2e-36 5 257 .. 907 1168 .] 905 1168 .] 0.82 Alignments for each domain: == domain 1 score: 111.2 bits; conditional E-value: 3.2e-36 Met_synt_B12 5 lveyidWtpffqaWelkgky.pkiledekvge.eakklfkdAqamLkkiieekllkakavvglfpAn 69 l ++dW + ++++ y k +++e++++ k+++ +++ +++ +ekl++ ++g +p++ lcl|NCBI__GCF_000186245.1:WP_013553448.1 907 LSMIFDWVNKRTLFKMHWGYkSKGMSKEEYQKlLDKTVYPAWERLKDTFLKEKLFEPTILYGYYPCR 973 56678999988999999888534455555555155566666667777899***************** PP Met_synt_B12 70 segddievyades....rse............elatlhtLrqqaekeegkpnlclaDfvapkesgvk 120 s+++++ +++ ++ +se + ++++ rq ++kp+++l+Df +++ ++ lcl|NCBI__GCF_000186245.1:WP_013553448.1 974 SDDQELFLFSPDEgwfsESEvnrepleeivgrAVGVFNFPRQ-----RRKPYRALSDFFRHE---RH 1032 **9999999555545431112222333222212333444444.....5789*********95...57 PP Met_synt_B12 121 DyiGlFavtaglgieelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsn 187 D+++l +v+ag +i e+ +++ ++ + + lv+ l LaeA+ae+ h+++r +l ++de + lcl|NCBI__GCF_000186245.1:WP_013553448.1 1033 DVVALTCVSAGPKITEYERALYEKGEYLEYNLVHGLGVELAEALAEVAHKQIRLDLGIASEDEGHTL 1099 *********************9999999999************************999999****** PP Met_synt_B12 188 eelikekYqgiRpApGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpeary 254 +++ ++Y+g R+++GY+acpd ++++ +f+ll+ ee gieL+e++ ++P++s ++++ hpea+y lcl|NCBI__GCF_000186245.1:WP_013553448.1 1100 RDVRMNRYRGARYSFGYAACPDLEQSRVIFDLLEPEE-FGIELSETFQIHPEQSTTAIVVHHPEATY 1165 *************************************.***************************** PP Met_synt_B12 255 Fav 257 +av lcl|NCBI__GCF_000186245.1:WP_013553448.1 1166 YAV 1168 *97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1168 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: 00:00:00.01 # Mc/sec: 21.04 // [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